Science.gov

Sample records for multiple binding modes

  1. Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes

    SciTech Connect

    C Simmons; C Magee; D Smith; L Lauman; J Chaput; J Allen

    2011-12-31

    The creation of synthetic enzymes with predefined functions represents a major challenge in future synthetic biology applications. Here, we describe six structures of de novo proteins that have been determined using protein crystallography to address how simple enzymes perform catalysis. Three structures are of a protein, DX, selected for its stability and ability to tightly bind ATP. Despite the addition of ATP to the crystallization conditions, the presence of a bound but distorted ATP was found only under excess ATP conditions, with ADP being present under equimolar conditions or when crystallized for a prolonged period of time. A bound ADP cofactor was evident when Asp was substituted for Val at residue 65, but ATP in a linear configuration is present when Phe was substituted for Tyr at residue 43. These new structures complement previously determined structures of DX and the protein with the Phe 43 to Tyr substitution [Simmons, C. R., et al. (2009) ACS Chem. Biol. 4, 649-658] and together demonstrate the multiple ADP/ATP binding modes from which a model emerges in which the DX protein binds ATP in a configuration that represents a transitional state for the catalysis of ATP to ADP through a slow, metal-free reaction capable of multiple turnovers. This unusual observation suggests that design-free methods can be used to generate novel protein scaffolds that are tailor-made for catalysis.

  2. On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data

    NASA Astrophysics Data System (ADS)

    Lewis, Paul J.; de Jonge, Marc; Daeyaert, Frits; Koymans, Luc; Vinkers, Maarten; Heeres, Jan; Janssen, Paul A. J.; Arnold, Eddy; Das, Kalyan; Clark, Art D., Jr.; Hughes, Stephen H.; Boyer, Paul L.; de Béthune, Marie-Pierre; Pauwels, Rudi; Andries, Koen; Kukla, Mike; Ludovici, Donald; De Corte, Bart; Kavash, Robert; Ho, Chih

    2003-02-01

    There are several indications that a given compound or a set of related compounds can bind in different modes to a specific binding site of a protein. This is especially evident from X-ray crystallographic structures of ligand-protein complexes. The availability of multiple binding modes of a ligand in a binding site may present an advantage in drug design when simultaneously optimizing several criteria. In the case of the design of anti-HIV compounds we observed that the more active compounds that are also resilient against mutation of the non-nucleoside binding site of HIV1-reverse transcriptase make use of more binding modes than the less active and resilient compounds.

  3. Multiple binding modes of substrate to the catalytic RNA subunit of RNase P from Escherichia coli.

    PubMed Central

    Pomeranz Krummel, D A; Altman, S

    1999-01-01

    M1 RNA that contained 4'-thiouridine was photochemically cross-linked to different substrates and to a product of the reaction it governs. The locations of the cross-links in these photochemically induced complexes were identified. The cross-links indicated that different substrates share some contacts but have distinct binding modes to M1 RNA. The binding of some substrates also results in a substrate-dependent conformational change in the enzymatic RNA, as evidenced by the appearance of an M1 RNA intramolecular cross-link. The identification of the cross-links between M1 RNA and product indicate that they are shared with only one of the three cross-linked E-S complexes that were identified, an indication of noncompetitive inhibition by the product. We also examined whether the cross-linked complexes between M1 RNA and substrate(s) or product are altered in the presence of the enzyme's protein cofactor (C5 protein) and in the presence of different concentrations of divalent metal ions. C5 protein enhanced the yield of certain M1 RNA-substrate cross-linked complexes for both wild-type M1 RNA and a deletion mutant of M1 RNA (delta[273-281]), but not for the M1 RNA-product complex. High concentrations of Mg2+ increased the yield of all M1 RNA-substrate complexes but not the M1 RNA-product complex. PMID:10445877

  4. Cross-class metallo-β-lactamase inhibition by bisthiazolidines reveals multiple binding modes

    PubMed Central

    Hinchliffe, Philip; González, Mariano M.; Mojica, Maria F.; González, Javier M.; Castillo, Valerie; Saiz, Cecilia; Kosmopoulou, Magda; Tooke, Catherine L.; Llarrull, Leticia I.; Mahler, Graciela; Bonomo, Robert A.; Vila, Alejandro J.; Spencer, James

    2016-01-01

    Metallo-β-lactamases (MBLs) hydrolyze almost all β-lactam antibiotics and are unaffected by clinically available β-lactamase inhibitors (βLIs). Active-site architecture divides MBLs into three classes (B1, B2, and B3), complicating development of βLIs effective against all enzymes. Bisthiazolidines (BTZs) are carboxylate-containing, bicyclic compounds, considered as penicillin analogs with an additional free thiol. Here, we show both l- and d-BTZ enantiomers are micromolar competitive βLIs of all MBL classes in vitro, with Kis of 6–15 µM or 36–84 µM for subclass B1 MBLs (IMP-1 and BcII, respectively), and 10–12 µM for the B3 enzyme L1. Against the B2 MBL Sfh-I, the l-BTZ enantiomers exhibit 100-fold lower Kis (0.26–0.36 µM) than d-BTZs (26–29 µM). Importantly, cell-based time-kill assays show BTZs restore β-lactam susceptibility of Escherichia coli-producing MBLs (IMP-1, Sfh-1, BcII, and GOB-18) and, significantly, an extensively drug-resistant Stenotrophomonas maltophilia clinical isolate expressing L1. BTZs therefore inhibit the full range of MBLs and potentiate β-lactam activity against producer pathogens. X-ray crystal structures reveal insights into diverse BTZ binding modes, varying with orientation of the carboxylate and thiol moieties. BTZs bind the di-zinc centers of B1 (IMP-1; BcII) and B3 (L1) MBLs via the free thiol, but orient differently depending upon stereochemistry. In contrast, the l-BTZ carboxylate dominates interactions with the monozinc B2 MBL Sfh-I, with the thiol uninvolved. d-BTZ complexes most closely resemble β-lactam binding to B1 MBLs, but feature an unprecedented disruption of the D120–zinc interaction. Cross-class MBL inhibition therefore arises from the unexpected versatility of BTZ binding. PMID:27303030

  5. Multiple Binding Modes between HNF4α and the LXXLL Motifs of PGC-1α Lead to Full Activation*

    PubMed Central

    Rha, Geun Bae; Wu, Guangteng; Shoelson, Steven E.; Chi, Young-In

    2009-01-01

    Hepatocyte nuclear factor 4α (HNF4α) is a novel nuclear receptor that participates in a hierarchical network of transcription factors regulating the development and physiology of such vital organs as the liver, pancreas, and kidney. Among the various transcriptional coregulators with which HNF4α interacts, peroxisome proliferation-activated receptor γ (PPARγ) coactivator 1α (PGC-1α) represents a novel coactivator whose activation is unusually robust and whose binding mode appears to be distinct from that of canonical coactivators such as NCoA/SRC/p160 family members. To elucidate the potentially unique molecular mechanism of PGC-1α recruitment, we have determined the crystal structure of HNF4α in complex with a fragment of PGC-1α containing all three of its LXXLL motifs. Despite the presence of all three LXXLL motifs available for interactions, only one is bound at the canonical binding site, with no additional contacts observed between the two proteins. However, a close inspection of the electron density map indicates that the bound LXXLL motif is not a selected one but an averaged structure of more than one LXXLL motif. Further biochemical and functional studies show that the individual LXXLL motifs can bind but drive only minimal transactivation. Only when more than one LXXLL motif is involved can significant transcriptional activity be measured, and full activation requires all three LXXLL motifs. These findings led us to propose a model wherein each LXXLL motif has an additive effect, and the multiple binding modes by HNF4α toward the LXXLL motifs of PGC-1α could account for the apparent robust activation by providing a flexible mechanism for combinatorial recruitment of additional coactivators and mediators. PMID:19846556

  6. New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA.

    PubMed

    Hou, Jin-Qiang; Chen, Shuo-Bin; Tan, Jia-Heng; Luo, Hai-Bin; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu

    2012-12-01

    G-quadruplexes are higher-order DNA and RNA structures formed from guanine-rich sequences. These structures have recently emerged as a new class of potential molecular targets for anticancer drugs. An understanding of the three-dimensional interactions between small molecular ligands and their G-quadruplex targets in solution is crucial for rational drug design and the effective optimization of G-quadruplex ligands. Thus far, rational ligand design has been focused mainly on the G-quartet platform. It should be noted that small molecules can also bind to loop nucleotides, as observed in crystallography studies. Hence, it would be interesting to elucidate the mechanism underlying how ligands in distinct binding modes influence the flexibility of G-quadruplex. In the present study, based on a crystal structure analysis, the models of a tetra-substituted naphthalene diimide ligand bound to a telomeric G-quadruplex with different modes were built and simulated with a molecular dynamics simulation method. Based on a series of computational analyses, the structures, dynamics, and interactions of ligand-quadruplex complexes were studied. Our results suggest that the binding of the ligand to the loop is viable in aqueous solutions but dependent on the particular arrangement of the loop. The binding of the ligand to the loop enhances the flexibility of the G-quadruplex, while the binding of the ligand simultaneously to both the quartet and the loop diminishes its flexibility. These results add to our understanding of the effect of a ligand with different binding modes on G-quadruplex flexibility. Such an understanding will aid in the rational design of more selective and effective G-quadruplex binding ligands.

  7. Mixed Mode Matrix Multiplication

    SciTech Connect

    Meng-Shiou Wu; Srinivas Aluru; Ricky A. Kendall

    2004-09-30

    In modern clustering environments where the memory hierarchy has many layers (distributed memory, shared memory layer, cache,...), an important question is how to fully utilize all available resources and identify the most dominant layer in certain computations. When combining algorithms on all layers together, what would be the best method to get the best performance out of all the resources we have? Mixed mode programming model that uses thread programming on the shared memory layer and message passing programming on the distributed memory layer is a method that many researchers are using to utilize the memory resources. In this paper, they take an algorithmic approach that uses matrix multiplication as a tool to show how cache algorithms affect the performance of both shared memory and distributed memory algorithms. They show that with good underlying cache algorithm, overall performance is stable. When underlying cache algorithm is bad, superlinear speedup may occur, and an increasing number of threads may also improve performance.

  8. Structure of the human angiotensin II type 1 (AT1) receptor bound to angiotensin II from multiple chemoselective photoprobe contacts reveals a unique peptide binding mode.

    PubMed

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel

    2013-03-22

    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs.

  9. Landscape of protein–small ligand binding modes

    PubMed Central

    Kinoshita, Kengo

    2016-01-01

    Abstract Elucidating the mechanisms of specific small‐molecule (ligand) recognition by proteins is a long‐standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein–ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all‐against‐all comparison of 20,040 protein–ligand complexes provided the landscape of the protein–ligand binding modes and its relationships with protein‐ and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R 2 = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein–ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them. PMID:27327045

  10. The central distribution of a corticotropin-releasing factor (CRF)-binding protein predicts multiple sites and modes of interaction with CRF.

    PubMed Central

    Potter, E; Behan, D P; Linton, E A; Lowry, P J; Sawchenko, P E; Vale, W W

    1992-01-01

    In recent studies to clone and characterize genes coding for the corticotropin-releasing factor-binding protein (CRF-BP), analysis of the tissue distribution of the CRF-BP gene indicated a high level of expression in the rat brain. We have now characterized by immunohistochemical and hybridization histochemical means the cellular localization of CRF-BP protein and mRNA expression, respectively. Results from both approaches converged to indicate that CRF-BP is expressed predominantly in the cerebral cortex, including all major archi-, paleo-, and neocortical fields. Other prominent sites of mRNA and protein expression include subcortical limbic system structures (amygdala, bed nucleus of the stria terminalis), sensory relays associated with the auditory, olfactory, vestibular, and trigeminal systems, severe raphe nuclei, and a number of cell groups in the brainstem reticular core. Expression in the hypothalamus appears largely limited to the ventral premammillary and dorsomedial nuclei; only isolated CRF-BP-stained cells are apparent in neurosecretory cell groups. Dual immunostaining for CRF and CRF-BP revealed a partial colocalization in some of these regions. In addition, prominent CRF-BP-stained terminal fields have been identified in association with CRF-expressing cell groups in circumscribed hypothalamic and limbic structures. In the anterior pituitary, CRF-BP mRNA and immunoreactivity were colocalized with corticotropin-immunoreactivity in a majority of corticotropes. Thus, CRF-BP could serve to modify the actions of CRF by intra- and intercellular mechanisms, in CRF-related pathways in the central nervous system and pituitary. Images PMID:1315056

  11. When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?

    PubMed

    Malhotra, Shipra; Karanicolas, John

    2017-01-12

    Traditional hit-to-lead optimization assumes that upon elaboration of chemical structure, the ligand retains its binding mode relative to the receptor. Here, we build a large-scale collection of related ligand pairs solved in complex with the same protein partner: we find that for 41 of 297 pairs (14%), the binding mode changes upon elaboration of the smaller ligand. While certain ligand physiochemical properties predispose changes in binding mode, particularly those properties that define fragments, simple structure-based modeling proves far more effective for identifying substitutions that alter the binding mode. Some ligand pairs change binding mode because the added substituent would irreconcilably conflict with the receptor in the original pose, whereas others change because the added substituent enables new, stronger interactions that are available only in a different pose. Scaffolds that can engage their target using alternate poses may enable productive structure-based optimization along multiple divergent pathways.

  12. Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay.

    PubMed

    McKnight, Ruel E; Gleason, Aaron B; Keyes, James A; Sahabi, Sadia

    2007-02-15

    A topoisomerase I DNA unwinding assay has been used to determine the relative DNA-binding affinities of a model pair of homologous naphthalene diimides. Binding affinity data were corroborated using calorimetric (ITC) and spectrophotometric (titration and T(m)) studies, with substituent size playing a significant role in binding. The assay was also used to investigate the mode of binding adopted by several known DNA-binding agents, including SYBR Green and PicoGreen. Some of the compounds exhibited unexpected binding modes.

  13. Multiple Mode Actuation of a Turbulent Jet

    NASA Technical Reports Server (NTRS)

    Pack, LaTunia G.; Seifert, Avi

    2001-01-01

    The effects of multiple mode periodic excitation on the evolution of a circular turbulent jet were studied experimentally. A short, wide-angle diffuser was attached to the jet exit. Streamwise and cross-stream excitations were introduced at the junction between the jet exit and the diffuser inlet on opposing sides of the jet. The introduction of high amplitude, periodic excitation in the streamwise direction enhances the mixing and promotes attachment of the jet shear-layer to the diffuser wall. Cross-stream excitation applied over a fraction of the jet circumference can deflect the jet away from the excitation slot. The two modes of excitation were combined using identical frequencies and varying the relative phase between the two actuators in search of an optimal response. It is shown that, for low and moderate periodic momentum input levels, the jet deflection angles depend strongly on the relative phase between the two actuators. Optimum performance is achieved when the phase difference is pi +/- pi/6. The lower effectiveness of the equal phase excitation is attributed to the generation of an azimuthally symmetric mode that does not produce the required non-axisymmetric vectoring. For high excitation levels, identical phase becomes more effective, while phase sensitivity decreases. An important finding was that with proper phase tuning, two unsteady actuators can be combined to obtain a non-linear response greater than the superposition of the individual effects.

  14. Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding.

    PubMed

    Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin; Kurepina, Natalia; Luan, Gan; Oppegard, Lisa M; Hiasa, Hiroshi; Marks, Kevin R; Kerns, Robert J; Berger, James M; Drlica, Karl

    2014-05-02

    DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys(466) gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly(81) and GyrB-Glu(466) residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases.

  15. Cooperative binding modes of Cu(II) in prion protein

    NASA Astrophysics Data System (ADS)

    Hodak, Miroslav; Chisnell, Robin; Lu, Wenchang; Bernholc, Jerry

    2007-03-01

    The misfolding of the prion protein, PrP, is responsible for a group of neurodegenerative diseases including mad cow disease and Creutzfeldt-Jakob disease. It is known that the PrP can efficiently bind copper ions; four high-affinity binding sites located in the octarepeat region of PrP are now well known. Recent experiments suggest that at low copper concentrations new binding modes, in which one copper ion is shared between two or more binding sites, are possible. Using our hybrid Thomas-Fermi/DFT computational scheme, which is well suited for simulations of biomolecules in solution, we investigate the geometries and energetics of two, three and four binding sites cooperatively binding one copper ion. These geometries are then used as inputs for classical molecular dynamics simulations. We find that copper binding affects the secondary structure of the PrP and that it stabilizes the unstructured (unfolded) part of the protein.

  16. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    PubMed

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  17. Predicting bioactive conformations and binding modes of macrocycles

    NASA Astrophysics Data System (ADS)

    Anighoro, Andrew; de la Vega de León, Antonio; Bajorath, Jürgen

    2016-10-01

    Macrocyclic compounds experience increasing interest in drug discovery. It is often thought that these large and chemically complex molecules provide promising candidates to address difficult targets and interfere with protein-protein interactions. From a computational viewpoint, these molecules are difficult to treat. For example, flexible docking of macrocyclic compounds is hindered by the limited ability of current docking approaches to optimize conformations of extended ring systems for pose prediction. Herein, we report predictions of bioactive conformations of macrocycles using conformational search and binding modes using docking. Conformational ensembles generated using specialized search technique of about 70 % of the tested macrocycles contained accurate bioactive conformations. However, these conformations were difficult to identify on the basis of conformational energies. Moreover, docking calculations with limited ligand flexibility starting from individual low energy conformations rarely yielded highly accurate binding modes. In about 40 % of the test cases, binding modes were approximated with reasonable accuracy. However, when conformational ensembles were subjected to rigid body docking, an increase in meaningful binding mode predictions to more than 50 % of the test cases was observed. Electrostatic effects did not contribute to these predictions in a positive or negative manner. Rather, achieving shape complementarity at macrocycle-target interfaces was a decisive factor. In summary, a combined computational protocol using pre-computed conformational ensembles of macrocycles as a starting point for docking shows promise in modeling binding modes of macrocyclic compounds.

  18. Detection and characterization of nonspecific, sparsely-populated binding modes in the early stages of complexation

    PubMed Central

    Cardone, A.; Bornstein, A.; Pant, H. C.; Brady, M.; Sriram, R.; Hassan, S. A.

    2015-01-01

    A method is proposed to study protein-ligand binding in a system governed by specific and non-specific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultra-weak associations lead instead to broader distributions, a manifestation of non-specific, sparsely-populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (pre-relaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. PMID:25782918

  19. Active control of multiple resistive wall modes

    NASA Astrophysics Data System (ADS)

    Brunsell, P. R.; Yadikin, D.; Gregoratto, D.; Paccagnella, R.; Liu, Y. Q.; Bolzonella, T.; Cecconello, M.; Drake, J. R.; Kuldkepp, M.; Manduchi, G.; Marchiori, G.; Marrelli, L.; Martin, P.; Menmuir, S.; Ortolani, S.; Rachlew, E.; Spizzo, G.; Zanca, P.

    2005-12-01

    A two-dimensional array of saddle coils at Mc poloidal and Nc toroidal positions is used on the EXTRAP T2R reversed-field pinch (Brunsell P R et al 2001 Plasma Phys. Control. Fusion 43 1457) to study active control of resistive wall modes (RWMs). Spontaneous growth of several RWMs with poloidal mode number m = 1 and different toroidal mode number n is observed experimentally, in agreement with linear MHD modelling. The measured plasma response to a controlled coil field and the plasma response computed using the linear circular cylinder MHD model are in quantitive agreement. Feedback control introduces a linear coupling of modes with toroidal mode numbers n, n' that fulfil the condition |n - n'| = Nc. Pairs of coupled unstable RWMs are present in feedback experiments with an array of Mc × Nc = 4 × 16 coils. Using intelligent shell feedback, the coupled modes are generally not controlled even though the field is suppressed at the active coils. A better suppression of coupled modes may be achieved in the case of rotating modes by using the mode control feedback scheme with individually set complex gains. In feedback with a larger array of Mc × Nc = 4 × 32 coils, the coupling effect largely disappears, and with this array, the main internal RWMs n = -11, -10, +5, +6 are all simultaneously suppressed throughout the discharge (7 8 wall times). With feedback there is a two-fold extension of the pulse length, compared to discharges without feedback.

  20. Multiple Modes of Inquiry in Earth Science

    ERIC Educational Resources Information Center

    Kastens, Kim A.; Rivet, Ann

    2008-01-01

    To help teachers enrich their students' understanding of inquiry in Earth science, this article describes six modes of inquiry used by practicing geoscientists (Earth scientists). Each mode of inquiry is illustrated by using examples of seminal or pioneering research and provides pointers to investigations that enable students to experience these…

  1. Observation of Protein Structural Vibrational Mode Sensitivity to Ligand Binding

    NASA Astrophysics Data System (ADS)

    Niessen, Katherine; Xu, Mengyang; Snell, Edward; Markelz, Andrea

    2014-03-01

    We report the first measurements of the dependence of large-scale protein intramolecular vibrational modes on ligand binding. These collective vibrational modes in the terahertz (THz) frequency range (5-100 cm-1) are of great interest due to their predicted relation to protein function. Our technique, Crystals Anisotropy Terahertz Microscopy (CATM), allows for room temperature, table-top measurements of the optically active intramolecular modes. CATM measurements have revealed surprisingly narrowband features. CATM measurements are performed on single crystals of chicken egg-white lysozyme (CEWL) as well as CEWL bound to tri-N-acetylglucosamine (CEWL-3NAG) inhibitor. We find narrow band resonances that dramatically shift with binding. Quasiharmonic calculations are performed on CEWL and CEWL-3NAG proteins with CHARMM using normal mode analysis. The expected CATM response of the crystals is then calculated by summing over all protein orientations within the unit cell. We will compare the CATM measurements with the calculated results and discuss the changes which arise with protein-ligand binding. This work is supported by NSF grant MRI 2 grant DBI2959989.

  2. Probing the binding mode of psoralen to calf thymus DNA.

    PubMed

    Zhou, Xiaoyue; Zhang, Guowen; Wang, Langhong

    2014-06-01

    The binding properties between psoralen (PSO) and calf thymus DNA (ctDNA) were predicted by molecular docking, and then determined with the use of UV-vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, coupled with DNA melting and viscosity measurements. The data matrix obtained from UV-vis spectra was resolved by multivariate curve resolution-alternating least squares (MCR-ALS) approach. The pure spectra and the equilibrium concentration profiles for PSO, ctDNA and PSO-ctDNA complex extracted from the highly overlapping composite response were obtained simultaneously to evaluate the PSO-ctDNA interaction. The intercalation mode of PSO binding to ctDNA was supported by the results from the melting studies, viscosity measurements, iodide quenching and fluorescence polarization experiments, competitive binding investigations and CD analysis. The molecular docking prediction showed that the specific binding most likely occurred between PSO and adenine bases of ctDNA. FT-IR spectra studies further confirmed that PSO preferentially bound to adenine bases, and this binding decreased right-handed helicity of ctDNA and enhanced the degree of base stacking with the preservation of native B-conformation. The calculated thermodynamic parameters indicated that hydrogen bonds and van der Waals forces played a major role in the binding process.

  3. Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1

    PubMed Central

    Wang, Zhanli; Sun, Lidan; Yu, Hui; Zhang, Yanhui; Gong, Wuzhuang; Jin, Hongwei; Zhang, Liangren; Liang, Huaping

    2012-01-01

    Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1 was still not fully understood. In this perspective, the homology models of TRPV1 were generated using the crystal structure of the voltage-dependent shaker family K+ channel as a template. We then performed docking and molecular dynamics simulation to gain a better understanding of the probable binding modes of evodiamine within the TRPV1 binding pocket. There are no significant interspecies differences in evodiamine binding in rat, human and rabbit TRPV1 models. Pharmacophore modeling further provided confidence for the validity of the docking studies. This study is the first to shed light on the structural determinants required for the interaction between TRPV1 and evodiamine, and gives new suggestions for the rational design of novel TRPV1 ligands. PMID:22942745

  4. Multiple movement modes by large herbivores at multiple spatiotemporal scales

    PubMed Central

    Fryxell, John M.; Hazell, Megan; Börger, Luca; Dalziel, Ben D.; Haydon, Daniel T.; Morales, Juan M.; McIntosh, Therese; Rosatte, Rick C.

    2008-01-01

    Recent theory suggests that animals should switch facultatively among canonical movement modes as a complex function of internal state, landscape characteristics, motion capacity, and navigational capacity. We tested the generality of this paradigm for free-ranging elk (Cervus elaphus) over 5 orders of magnitude in time (minutes to years) and space (meters to 100 km). At the coarsest spatiotemporal scale, elk shifted from a dispersive to a home-ranging phase over the course of 1–3 years after introduction into a novel environment. At intermediate spatiotemporal scales, elk continued to alternate between movement modes. During the dispersive phase, elk alternated between encamped and exploratory modes, possibly linked to changes in motivational goals from foraging to social bonding. During the home-ranging phase, elk movements were characterized by a complex interplay between attraction to preferred habitat types and memory of previous movements across the home-range. At the finest temporal and spatial scale, elk used area-restricted search while browsing, interspersed with less sinuous paths when not browsing. Encountering a patch of high-quality food plants triggered the switch from one mode to the next, creating biphasic movement dynamics that were reinforced by local resource heterogeneity. These patterns suggest that multiphasic structure is fundamental to the movement patterns of elk at all temporal and spatial scales tested. PMID:19060190

  5. Binding of ethidium to the nucleosome core particle. 2. Internal and external binding modes

    SciTech Connect

    McMurray, C.T.; Small, E.W.; van Holde, K.E. )

    1991-06-11

    The authors have previously reported that the binding of ethidium bromide to the nucleosome core particle results in a stepwise dissociation of the structure which involves the initial release of one copy each of H2A and H2B. In this report, they have examined the absorbance and fluorescence properties of intercalated and outside bound forms of ethidium bromide. From these properties, they have measured the extent of external, electrostatic binding of the dye versus internal, intercalation binding to the core particle, free from contribution by linker DNA. They have established that dissociation is induced by the intercalation mode of binding to DNA within the core particle DNA, and not by binding to the histones or by nonintercalative binding to DNA. The covalent binding of ({sup 3}H)-8-azidoethidium to the core particle clearly shows that < 1.0 adduct is formed per histone octamer over a wide range of input ratios. Simultaneously, analyses of steady-state fluorescence enhancement and fluorescence lifetime data from bound ethidium complexes demonstrate extensive intercalation binding. Combined analyses from steady-state fluorescence intensity with equilibrium dialysis or fluorescence lifetime data revealed that dissociation began when {approximately}14 ethidium molecules are bound by intercalation to each core particle and < 1.0 nonintercalated ion pair was formed per core particle.

  6. Structural system reliability under multiple failure modes

    NASA Technical Reports Server (NTRS)

    Mahadevan, S.; Chamis, C. C.

    1993-01-01

    This paper describes a computational method for system reliability estimation of propulsion structures. The failure domain of the entire structural system is computed through the union of failure regions for various critical system failure modes. The effect of non-critical progressive damage is incorporated through structural reanalysis, resulting in the construction of several linear segments to approximately cover the system failure domain. An adaptive damage imposition scheme is outlined for the sake of computational efficiency. The proposed method is used to construct the system survival cdf (cumulative distribution function) of a two-rotor system.

  7. The Unique Binding Mode of Laulimalide to Two Tubulin Protofilaments.

    PubMed

    Churchill, Cassandra D M; Klobukowski, Mariusz; Tuszynski, Jack A

    2015-08-01

    Laulimalide, a cancer chemotherapeutic in preclinical development, has a unique binding site located on two adjacent β-tubulin units between tubulin protofilaments of a microtubule. Our extended protein model more accurately mimics the microtubule environment, and together with a 135 ns molecular dynamics simulation, identifies a new binding mode for laulimalide, which differs from the modes presented in work using smaller protein models. The new laulimalide-residue interactions that are computationally revealed explain the contacts observed via independent mass shift perturbation experiments. The inclusion of explicit solvent shows that many laulimalide-tubulin interactions are water mediated. The new contacts between the drug and the microtubule structure not only improve our understanding of laulimalide binding but also will be essential for efficient derivatization and optimization of this prospective cancer chemotherapy agent. Observed changes in secondary protein structure implicate the S7-H9 loop (M-loop) and H1'-S2 loop in the mechanism by which laulimalide stabilizes microtubules to exert its cytotoxic effects.

  8. Detection and quantitative analysis of two independent binding modes of a small ligand responsible for DC-SIGN clustering.

    PubMed

    Guzzi, C; Alfarano, P; Sutkeviciute, I; Sattin, S; Ribeiro-Viana, R; Fieschi, F; Bernardi, A; Weiser, J; Rojo, J; Angulo, J; Nieto, P M

    2016-01-07

    DC-SIGN (dendritic cell-specific ICAM-3 grabbing non-integrin) is a C-type lectin receptor (CLR) present, mainly in dendritic cells (DCs), as one of the major pattern recognition receptors (PRRs). This receptor has a relevant role in viral infection processes. Recent approaches aiming to block DC-SIGN have been presented as attractive anti-HIV strategies. DC-SIGN binds mannose or fucose-containing carbohydrates from viral proteins such as the HIV envelope glycoprotein gp120. We have previously demonstrated that multivalent dendrons bearing multiple copies of glycomimetic ligands were able to inhibit DC-SIGN-dependent HIV infection in cervical explant models. Optimization of glycomimetic ligands requires detailed characterization and analysis of their binding modes because they notably influence binding affinities. In a previous study we characterized the binding mode of DC-SIGN with ligand 1, which shows a single binding mode as demonstrated by NMR and X-ray crystallography. In this work we report the binding studies of DC-SIGN with pseudotrisaccharide 2, which has a larger affinity. Their binding was analysed by TR-NOESY and STD NMR experiments, combined with the CORCEMA-ST protocol and molecular modelling. These studies demonstrate that in solution the complex cannot be explained by a single binding mode. We describe the ensemble of ligand bound modes that best fit the experimental data and explain the higher inhibition values found for ligand 2.

  9. Simultaneous demultiplexing and steering of multiple orbital angular momentum modes

    PubMed Central

    Li, Shuhui; Wang, Jian

    2015-01-01

    We present a simple scheme to perform simultaneous demultiplexing and steering of multiple orbital angular momentum (OAM) modes using a single complex phase mask. By designing the phase mask, the propagation directions of demultiplexed beams can be arbitrarily steered. System experiments using orthogonal frequency-division multiplexing 32-ary quadrature amplitude modulation (OFDM-32QAM) signals over two OAM modes are carried out by using a two-mode complex phase mask. Moreover, demultiplexing of sixteen OAM modes and arbitrary demultiplexed beam steering are also demonstrated in the experiment. PMID:26503167

  10. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes

    PubMed Central

    Affaticati, Pierre E.; Dai, Shao-Bo; Payongsri, Panwajee; Hailes, Helen C.; Tittmann, Kai; Dalby, Paul A.

    2016-01-01

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies. PMID:27767080

  11. Multiple ion temperature gradient driven modes in transport barriers

    NASA Astrophysics Data System (ADS)

    Han, M. K.; Wang, Zheng-Xiong; Dong, J. Q.; Du, Huarong

    2017-04-01

    The ion temperature gradient (ITG) modes in transport barriers (TBs) of tokamak plasmas are numerically studied with a code solving gyrokinetic integral eigenvalue equations in toroidal configurations. It is found that multiple ITG modes with conventional and unconventional ballooning mode structures can be excited simultaneously in TBs with steep gradients of ion temperature and density. The characteristics of the modes, including the dependence of the mode frequencies, growth rate and structure on plasma parameters, are systematically investigated. Unconventional modes with large mode-number l (where l denotes a certain parity and peak number in ballooning space) dominate in the large {{k}θ}{ρs} region ({{k}θ}{ρs}≥slant 1.2 ), while the conventional mode with l=0 dominates in the medium {{k}θ}{ρs} region (0.4≤slant {{k}θ}{ρs}<1.2 ), and unconventional modes with small mode-number l dominate in the small {{k}θ}{ρs} region ({{k}θ}{ρs}<0.4 ). Thus, the {{k}θ}{ρs} spectra of these conventional and unconventional modes at steep gradients are qualitatively different from those of the conventional ITG modes at small or medium gradients, in which the growth rate of the only ITG mode with l=0 reaches maximum at the medium value {{k}θ}{ρs}=0.6 . Through scanning ion temperature gradient {{\\varepsilon}T\\text{i}} and density gradient {{\\varepsilon}n} separately, it is proven that the synergetic effect of {{\\varepsilon}T\\text{i}} and {{\\varepsilon}n} , rather than {{\\varepsilon}T\\text{i}} alone, drives the unconventional ITG modes in TBs. Moreover, it is found that the critical value of {{\\varepsilon}n} for driving the unconventional ITG modes with large l number increases with increasing {{k}θ}{ρs} . In addition, the effects of magnetic shear on conventional and unconventional ITG modes in the high confinement regime (H-mode) are analyzed in detail, and compared with equivalent effects on conventional modes in the low and intermediate gradient

  12. Equilibrium absorptive partitioning theory between multiple aerosol particle modes

    NASA Astrophysics Data System (ADS)

    Crooks, Matthew; Connolly, Paul; Topping, David; McFiggans, Gordon

    2016-10-01

    An existing equilibrium absorptive partitioning model for calculating the equilibrium gas and particle concentrations of multiple semi-volatile organics within a bulk aerosol is extended to allow for multiple involatile aerosol modes of different sizes and chemical compositions. In the bulk aerosol problem, the partitioning coefficient determines the fraction of the total concentration of semi-volatile material that is in the condensed phase of the aerosol. This work modifies this definition for multiple polydisperse aerosol modes to account for multiple condensed concentrations, one for each semi-volatile on each involatile aerosol mode. The pivotal assumption in this work is that each aerosol mode contains an involatile constituent, thus overcoming the potential problem of smaller particles evaporating completely and then condensing on the larger particles to create a monodisperse aerosol at equilibrium. A parameterisation is proposed in which the coupled non-linear system of equations is approximated by a simpler set of equations obtained by setting the organic mole fraction in the partitioning coefficient to be the same across all modes. By perturbing the condensed masses about this approximate solution a correction term is derived that accounts for many of the removed complexities. This method offers a greatly increased efficiency in calculating the solution without significant loss in accuracy, thus making it suitable for inclusion in large-scale models.

  13. Multiprocessor system with multiple concurrent modes of execution

    SciTech Connect

    Ahn, Daniel; Ceze, Luis H.; Chen, Dong Chen; Gara, Alan; Heidelberger, Philip; Ohmacht, Martin

    2016-11-22

    A multiprocessor system supports multiple concurrent modes of speculative execution. Speculation identification numbers (IDs) are allocated to speculative threads from a pool of available numbers. The pool is divided into domains, with each domain being assigned to a mode of speculation. Modes of speculation include TM, TLS, and rollback. Allocation of the IDs is carried out with respect to a central state table and using hardware pointers. The IDs are used for writing different versions of speculative results in different ways of a set in a cache memory.

  14. Multiprocessor system with multiple concurrent modes of execution

    DOEpatents

    Ahn, Daniel; Ceze, Luis H; Chen, Dong; Gara, Alan; Heidelberger, Philip; Ohmacht, Martin

    2013-12-31

    A multiprocessor system supports multiple concurrent modes of speculative execution. Speculation identification numbers (IDs) are allocated to speculative threads from a pool of available numbers. The pool is divided into domains, with each domain being assigned to a mode of speculation. Modes of speculation include TM, TLS, and rollback. Allocation of the IDs is carried out with respect to a central state table and using hardware pointers. The IDs are used for writing different versions of speculative results in different ways of a set in a cache memory.

  15. Multiple ligand simultaneous docking: orchestrated dancing of ligands in binding sites of protein.

    PubMed

    Li, Huameng; Li, Chenglong

    2010-07-30

    Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively.

  16. Effects of Multiple Resistive Walls and Mode Coupling on Mode Locking in RFPs

    NASA Astrophysics Data System (ADS)

    Guo, S. C.; Chu, M. S.

    2001-10-01

    Locked dynamo modes give rise to a serious deterioration of confinement at the plasma edge during the high current phase of reversed field pinches (RFP) operations. This is caused by the large braking torque exerted by the eddy currents on the resistive vacuum vessel on the dynamo modes1. The torque is strong enough to reduce the rotation frequency to an extremely small value. These tearing modes are then readily stopped (wall-locked) by a small external fixed error field. Several RFP devices are equipped with one or two thin (or thick) shells outside the vessel. This can, in principle, alleviate the locked mode problem. The present work presents a systematic calculation of the braking torques of multiple resistive walls (including both thin and thick shells) on a rotating tearing mode. The evolution of the frequency and the amplitude of a single representative tearing mode under the effect of multiple resistive walls is investigated. Numerical examples are provided for the modified RFX and other relevant devices. Generalization to the case of multiple(three) coupled modes and in the presence of externally applied helical rotating magnetic field2 will also be presented. 1. R. Fitzpatrick, S.C. Guo, D. J. Den Hartog and C. C. Hegna; Phys. of Plasmas, 6(10) 3878 (1999). 2. S. C. Guo and M. S. Chu; Phys. of Plasmas, 8(7) 3342 (2001).

  17. Broadband multiple responses of surface modes in quasicrystalline plasmonic structure

    PubMed Central

    Yuan, Haiming; Jiang, Xiangqian; Huang, Feng; Sun, Xiudong

    2016-01-01

    We numerically study the multiple excitation of surface modes in 2D photonic quasicrystal/metal/substrate structure. An improved rigorous coupled wave analysis method that can handle the quasicrystalline structure is presented. The quasicrystalline lattice, which refers to Penrose tiling in this paper, is generated by the cut-and-project method. The normal incidence spectrum presents a broadband multiple responses property. We find that the phase matching condition determines the excitation frequency for a given incident angle, while the depth of the reflection valley depends on the incident polarization. The modes will split into several sub-modes at oblique incidence, which give rise to the appearance of more responses on the spectrum. PMID:27492782

  18. Charging system with galvanic isolation and multiple operating modes

    SciTech Connect

    Kajouke, Lateef A.; Perisic, Milun; Ransom, Ray M.

    2013-01-08

    Systems and methods are provided for operating a charging system with galvanic isolation adapted for multiple operating modes. A vehicle charging system comprises a DC interface, an AC interface, a first conversion module coupled to the DC interface, and a second conversion module coupled to the AC interface. An isolation module is coupled between the first conversion module and the second conversion module. The isolation module comprises a transformer and a switching element coupled between the transformer and the second conversion module. The transformer and the switching element are cooperatively configured for a plurality of operating modes, wherein each operating mode of the plurality of operating modes corresponds to a respective turns ratio of the transformer.

  19. Multiple intersection properties of optical resonance modes in metallic metamaterials

    NASA Astrophysics Data System (ADS)

    Tokuda, Yasunori; Sakaguchi, Koichiro; Yamaguchi, Yuki; Takano, Keisuke

    2017-03-01

    Unusual behavior of Fabry-Perot-like waveguide resonance modes is presented for a quasi-dielectric metamaterial that consists of two metallic sub-wavelength cut-through slit-array slabs separated by an air-gap region. Simulations based on the finite-difference time-domain method were conducted. The unique optical properties were interpreted in terms of multiple intersection of the resonance modes. Depending on the intersection conditions of the optical modes, furthermore, a variety of crossing characteristics, i.e., fade-out crossing with/without an isolated loop, anticrossing with/without intensity reduction, and anticrossing with/without frequency repulsion, were identified for the air-gap dependence of the transmission spectra. These findings, which were obtained by careful observation of the properties of this type of metamaterial, present a novel and interesting aspect of the behavior of the optical resonance modes.

  20. Multiple Surface Plasmon Modes for Gold/Silver Alloy Nanorods

    SciTech Connect

    Bok, Hye-Mi; Shuford, Kevin L; Kim, Sungwan; Kim, Seong Kyu; Park, Sungho

    2009-01-01

    Alloy nanorods consisting of bimetallic gold and silver are synthesized by employing the electrochemical codeposition of Au/Ag alloy materials into the pores of anodized aluminum oxide templates. This paper presents the variation of localized surface plasmon resonance (LSPR) modes of the Au{sub x}/Ag{sub 1-x} alloy nanorods as a function of relative compositions of Au and Ag. Transverse and multiple longitudinal modes were observed when the length was longer than ca. 300 nm. For a given length, the transverse LSPR mode systematically blue-shifted as the Ag portion increased, while there was little variation in peak positions of the longitudinal LSPR modes. The optical properties of the Au{sub x}/Ag{sub 1-x} alloy nanorods were calculated using the discrete dipole approximation and showed a good agreement with the experimental measurements.

  1. Acyl-CoA binding proteins: multiplicity and function.

    PubMed

    Gossett, R E; Frolov, A A; Roths, J B; Behnke, W D; Kier, A B; Schroeder, F

    1996-09-01

    The physiological role of long-chain fatty acyl-CoA is thought to be primarily in intermediary metabolism of fatty acids. However, recent data show that nM to microM levels of these lipophilic molecules are potent regulators of cell functions in vitro. Although long-chain fatty acyl-CoA are present at several hundred microM concentration in the cell, very little long-chain fatty acyl-CoA actually exists as free or unbound molecules, but rather is bound with high affinity to membrane lipids and/or proteins. Recently, there is growing awareness that cytosol contains nonenzymatic proteins also capable of binding long-chain fatty acyl-CoA with high affinity. Although the identity of the cytosolic long-chain fatty acyl-CoA binding protein(s) has been the subject of some controversy, there is growing evidence that several diverse nonenzymatic cytosolic proteins will bind long-chain fatty acyl-CoA. Not only does acyl-CoA binding protein specifically bind medium and long-chain fatty acyl-CoA (LCFA-CoA), but ubiquitous proteins with multiple ligand specificities such as the fatty acid binding proteins and sterol carrier protein-2 also bind LCFA-CoA with high affinity. The potential of these acyl-CoA binding proteins to influence the level of free LCFA-CoA and thereby the amount of LCFA-CoA bound to regulatory sites in proteins and enzymes is only now being examined in detail. The purpose of this article is to explore the identity, nature, function, and pathobiology of these fascinating newly discovered long-chain fatty acyl-CoA binding proteins. The relative contributions of these three different protein families to LCFA-CoA utilization and/or regulation of cellular activities are the focus of new directions in this field.

  2. Dystrophin contains multiple independent membrane-binding domains.

    PubMed

    Zhao, Junling; Kodippili, Kasun; Yue, Yongping; Hakim, Chady H; Wasala, Lakmini; Pan, Xiufang; Zhang, Keqing; Yang, Nora N; Duan, Dongsheng; Lai, Yi

    2016-09-01

    Dystrophin is a large sub-sarcolemmal protein. Its absence leads to Duchenne muscular dystrophy (DMD). Binding to the sarcolemma is essential for dystrophin to protect muscle from contraction-induced injury. It has long been thought that membrane binding of dystrophin depends on its cysteine-rich (CR) domain. Here, we provide in vivo evidence suggesting that dystrophin contains three additional membrane-binding domains including spectrin-like repeats (R)1-3, R10-12 and C-terminus (CT). To systematically study dystrophin membrane binding, we split full-length dystrophin into ten fragments and examined subcellular localizations of each fragment by adeno-associated virus-mediated gene transfer. In skeletal muscle, R1-3, CR domain and CT were exclusively localized at the sarcolemma. R10-12 showed both cytosolic and sarcolemmal localization. Importantly, the CR-independent membrane binding was conserved in murine and canine muscles. A critical function of the CR-mediated membrane interaction is the assembly of the dystrophin-associated glycoprotein complex (DGC). While R1-3 and R10-12 did not restore the DGC, surprisingly, CT alone was sufficient to establish the DGC at the sarcolemma. Additional studies suggest that R1-3 and CT also bind to the sarcolemma in the heart, though relatively weak. Taken together, our study provides the first conclusive in vivo evidence that dystrophin contains multiple independent membrane-binding domains. These structurally and functionally distinctive membrane-binding domains provide a molecular framework for dystrophin to function as a shock absorber and signaling hub. Our results not only shed critical light on dystrophin biology and DMD pathogenesis, but also provide a foundation for rationally engineering minimized dystrophins for DMD gene therapy.

  3. A multiple work mode YAG laser in derma surgery

    NASA Astrophysics Data System (ADS)

    Sa, Yu; Zhang, Guizhong; Ye, Zhisheng; Yu, Lin

    2006-06-01

    It has been very common that a pulse laser is used in derma surgery based on the theory of "Selective Photothermolysis". This method has also been accepted as the best way to treat the pigments by the medical textbook. A kind of double-pulsed laser which gets the name by two pulse output at one pumping process is developed for derma surgery lately, and this kind of laser has been proved more effective and safe than single-pulse laser. We also develop a multiple work mode YAG laser including two double-pulsed modes at 1064nm and 532nm, two single-pulsed modes at 1064nm and 532nm, and one free-running mode at 1064nm. Considering availability, security and reliability of the laser as a surgery machine, some important subsystems of the laser are optimized carefully, such as Q-switch driver, wavelength-switching system, power supply, and control system etc. At last we get a prototype laser which can run for longer than 30 minutes continuously, and output Max10 pulse per second (pps) with Max800mJ energy at 1064nm double Q-Switch mode, or Max400mJ at 532nm. Using double pulse mode of the laser we do some removal experiments of tattoos and other pigments, and obtain good effect.

  4. Multiplicity counting from fission chamber signals in the current mode

    NASA Astrophysics Data System (ADS)

    Pázsit, I.; Pál, L.; Nagy, L.

    2016-12-01

    In nuclear safeguards, estimation of sample parameters using neutron-based non-destructive assay methods is traditionally based on multiplicity counting with thermal neutron detectors in the pulse mode. These methods in general require multi-channel analysers and various dead time correction methods. This paper proposes and elaborates on an alternative method, which is based on fast neutron measurements with fission chambers in the current mode. A theory of "multiplicity counting" with fission chambers is developed by incorporating Böhnel's concept of superfission [1] into a master equation formalism, developed recently by the present authors for the statistical theory of fission chamber signals [2,3]. Explicit expressions are derived for the first three central auto- and cross moments (cumulants) of the signals of up to three detectors. These constitute the generalisation of the traditional Campbell relationships for the case when the incoming events represent a compound Poisson distribution. Because now the expressions contain the factorial moments of the compound source, they contain the same information as the singles, doubles and triples rates of traditional multiplicity counting. The results show that in addition to the detector efficiency, the detector pulse shape also enters the formulas; hence, the method requires a more involved calibration than the traditional method of multiplicity counting. However, the method has some advantages by not needing dead time corrections, as well as having a simpler and more efficient data processing procedure, in particular for cross-correlations between different detectors, than the traditional multiplicity counting methods.

  5. Reusable Launch Vehicle Control In Multiple Time Scale Sliding Modes

    NASA Technical Reports Server (NTRS)

    Shtessel, Yuri; Hall, Charles; Jackson, Mark

    2000-01-01

    A reusable launch vehicle control problem during ascent is addressed via multiple-time scaled continuous sliding mode control. The proposed sliding mode controller utilizes a two-loop structure and provides robust, de-coupled tracking of both orientation angle command profiles and angular rate command profiles in the presence of bounded external disturbances and plant uncertainties. Sliding mode control causes the angular rate and orientation angle tracking error dynamics to be constrained to linear, de-coupled, homogeneous, and vector valued differential equations with desired eigenvalues placement. Overall stability of a two-loop control system is addressed. An optimal control allocation algorithm is designed that allocates torque commands into end-effector deflection commands, which are executed by the actuators. The dual-time scale sliding mode controller was designed for the X-33 technology demonstration sub-orbital launch vehicle in the launch mode. Simulation results show that the designed controller provides robust, accurate, de-coupled tracking of the orientation angle command profiles in presence of external disturbances and vehicle inertia uncertainties. This is a significant advancement in performance over that achieved with linear, gain scheduled control systems currently being used for launch vehicles.

  6. Tearing mode instability in a multiple current sheet system

    NASA Technical Reports Server (NTRS)

    Yan, M.; Otto, A.; Muzzell, D.; Lee, L. C.

    1994-01-01

    The tearing mode and magnetic reconnection are studied for multiple current sheet systems by two-dimensional magnetohydrodynamic (MHD) simulations. Both the linear and nonlinear evolution of this process are anaylsed for laminar perturbations. The results illustrate the existence of a linear regime with a symmetric and antisymmetric mode and agree with previous analytic results (Otto and Birk, 1992). The nonlinear evolution shows a number of interesting new features and may explain some properties in corresponding studies of turbulent reconnection. For wavelengths larger than twice the current sheet separation the evolution of antisymmetric modes leads to an entire reconfiguration of the magnetic field and converts a major portion of the magnetic energy into kinetic energy. Antisymmetric modes with smaller wavelengths and symmetric modes are found to saturate. The influence of the value of the resistivity on the reconnection rate decreases in the nonlinear evolution, and the ratio of current sheet separation to wavelength seems to be of major importance. A comparion of the dynamics of periodic current sheets with the evolution of only two current sheets indicates that some of the results for the periodic system also apply to the evolution of only two interacting current sheets. The results are discussed with respect to observations of large-scale plasma and magnetic field reconfigurations in the magnetosheath and near the Earth's bow shock.

  7. Multiple Modes of Ryanodine Receptor 2 Inhibition by Flecainide

    PubMed Central

    Mehra, D.; Imtiaz, M. S.; van Helden, D. F.; Knollmann, B. C.

    2014-01-01

    Catecholaminergic polymorphic ventricular tachycardia (CPVT) causes sudden cardiac death due to mutations in cardiac ryanodine receptors (RyR2), calsequestrin, or calmodulin. Flecainide, a class I antiarrhythmic drug, inhibits Na+ and RyR2 channels and prevents CPVT. The purpose of this study is to identify inhibitory mechanisms of flecainide on RyR2. RyR2 were isolated from sheep heart, incorporated into lipid bilayers, and investigated by single-channel recording under various activating conditions, including the presence of cytoplasmic ATP (2 mM) and a range of cytoplasmic [Ca2+], [Mg2+], pH, and [caffeine]. Flecainide applied to either the cytoplasmic or luminal sides of the membrane inhibited RyR2 by two distinct modes: 1) a fast block consisting of brief substate and closed events with a mean duration of ∼1 ms, and 2) a slow block consisting of closed events with a mean duration of ∼1 second. Both inhibition modes were alleviated by increasing cytoplasmic pH from 7.4 to 9.5 but were unaffected by luminal pH. The slow block was potentiated in RyR2 channels that had relatively low open probability, whereas the fast block was unaffected by RyR2 activation. These results show that these two modes are independent mechanisms for RyR2 inhibition, both having a cytoplasmic site of action. The slow mode is a closed-channel block, whereas the fast mode blocks RyR2 in the open state. At diastolic cytoplasmic [Ca2+] (100 nM), flecainide possesses an additional inhibitory mechanism that reduces RyR2 burst duration. Hence, multiple modes of action underlie RyR2 inhibition by flecainide. PMID:25274603

  8. Long-range optical binding in a hollow-core photonic crystal fiber using higher order modes

    NASA Astrophysics Data System (ADS)

    Bykov, Dmitry S.; Zeltner, Richard; Euser, Tijmen G.; Xie, Shangran; Russell, Philip St. J.

    2016-09-01

    We report long-range optical binding of multiple polystyrene nanoparticles (100-600 nm in diameter) at fixed interparticle distances that match multiples of the half-beat-lengths between the lowest order modes of a hollow-core photonic crystal fiber. Analysis suggests that each nanoparticle converts the incoming optical mode into a superposition of co-propagating modes, within the beat pattern of which further particles can become trapped. Strikingly, the entire particle arrangement can be moved over a distance of several cm, without changing the inter-particle spacing, by altering the ratio of backward-to-forward optical power. Potential applications are in multi-dimensional nanoparticle-based quantum optomechanical systems.

  9. Multiple modes of chromatin remodeling by Forkhead box proteins.

    PubMed

    Lalmansingh, Avin S; Karmakar, Sudipan; Jin, Yetao; Nagaich, Akhilesh K

    2012-07-01

    Forkhead box (FOX) proteins represent a large family of transcriptional regulators unified by their DNA binding domain (DBD) known as a 'forkhead' or 'winged helix' domain. Over 40 FOX genes have been identified in the mammalian genome. FOX proteins share significant sequence similarities in the DBD which allow them to bind to a consensus DNA response element. However, their modes of action are quite diverse as they regulate gene expression by acting as pioneer factors, transcription factors, or both. This review focuses on the mechanisms of chromatin remodeling with an emphasis on three sub-classes-FOXA, FOXO, and FOXP members. FOXA proteins serve as pioneer factors to open up local chromatin structure and thereby increase accessibility of chromatin to factors regulating transcription. FOXP proteins, in contrast, function as classic transcription factors to recruit a variety of chromatin modifying enzymes to regulate gene expression. FOXO proteins represent a hybrid subclass having dual roles as pioneering factors and transcription factors. A subset of FOX proteins interacts with condensed mitotic chromatin and may function as 'bookmarking' agents to maintain transcriptional competence at specific genomic sites. The overall diversity in chromatin remodeling function by FOX proteins is related to unique structural motifs present within the DBD flanking regions that govern selective interactions with core histones and/or chromatin coregulatory proteins. This article is part of a Special Issue entitled: Chromatin in time and space.

  10. Digital Real-Time Multiple Channel Multiple Mode Neutron Flux Estimation on FPGA-based Device

    NASA Astrophysics Data System (ADS)

    Thevenin, Mathieu; Barbot, Loïc; Corre, Gwénolé; Woo, Romuald; Destouches, Christophe; Normand, Stéphane

    2016-02-01

    This paper presents a complete custom full-digital instrumentation device that was designed for real-time neutron flux estimation, especially for nuclear reactor in-core measurement using subminiature Fission Chambers (FCs). Entire fully functional small-footprint design (about 1714 LUTs) is implemented on FPGA. It enables real-time acquisition and analysis of multiple channels neutron's flux both in counting mode and Campbelling mode. Experimental results obtained from this brand new device are consistent with simulation results and show good agreement within good uncertainty. This device paves the way for new applications perspectives in real-time nuclear reactor monitoring.

  11. Theoretical studies on binding modes of copper-based nucleases with DNA.

    PubMed

    Liu, Chunmei; Zhu, Yanyan; Tang, Mingsheng

    2016-03-01

    In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.

  12. Multiple periodicities in the solar magnetic field - Possible origin in a multiple-mode solar dynamo

    NASA Technical Reports Server (NTRS)

    Boyer, D. W.; Levy, E. H.

    1992-01-01

    The solar magnetic field is generated in an oscillatory mode with a 22 yr full period and gives rise to the 11 yr sunspot cycle. However, analyses of contemporary solar records, as well as other surrogate indicators of solar activity, suggest the presence also of longer term periodicities in the solar magnetic cycle. This paper suggests that the solar dynamo can operate in a multiply periodic state, with several periodicites being generated simultaneously at different depths in the convection zone. A simple two-layer model of the solar convection zone is used to illustrate the physical mechanism of spatially localized, multiple-periodicity-mode dynamo regeneration. The two layers are characterized by differences in their respective turbulent magnetic diffusivities. Although the magnetic modes interact with one another, each mode is produced large in one layer or the other, and has an oscillation period approximately equal to the time characteristic of magnetic diffusion across the layer. The observed complicated periodicity pattern in the solar magnetic field could be a combination of two (or more) dynamo modes generated in this manner. The calculations are carried out using a differential rotation model consistent with recent helioseismological measurements, illustrating the challenge to dynamo theory raised by those observational results.

  13. Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors

    PubMed Central

    Lee, Hui Sun; Jo, Sunhwan; Lim, Hyun-Suk; Im, Wonpil

    2012-01-01

    Molecular docking is widely used to obtain binding modes and binding affinities of a molecule to a given target protein. Despite considerable efforts, however, prediction of both properties by docking remains challenging mainly due to protein’s structural flexibility and inaccuracy of scoring functions. Here, an integrated approach has been developed to improve the accuracy of binding mode and affinity prediction, and tested for small molecule MDM2 and MDMX antagonists. In this approach, initial candidate models selected from docking are subjected to equilibration MD simulations to further filter the models. Free energy perturbation molecular dynamics (FEP/MD) simulations are then applied to the filtered ligand models to enhance the ability in predicting the near-native ligand conformation. The calculated binding free energies for MDM2 complexes are overestimated compared to experimental measurements mainly due to the difficulties in sampling highly flexible apo-MDM2. Nonetheless, the FEP/MD binding free energy calculations are more promising for discriminating binders from nonbinders than docking scores. In particular, the comparison between the MDM2 and MDMX results suggests that apo-MDMX has lower flexibility than apo-MDM2. In addition, the FEP/MD calculations provide detailed information on the different energetic contributions to ligand binding, leading to a better understanding of the sensitivity and specificity of protein-ligand interactions. PMID:22731511

  14. Molecular level studies on binding modes of labeling molecules with polyalanine peptides

    NASA Astrophysics Data System (ADS)

    Mao, Xiaobo; Wang, Chenxuan; Ma, Xiaojing; Zhang, Min; Liu, Lei; Zhang, Lan; Niu, Lin; Zeng, Qindao; Yang, Yanlian; Wang, Chen

    2011-04-01

    In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloidpeptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalaninepeptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalaninepeptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloidpeptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalaninepeptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalaninepeptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides. Electronic

  15. Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides

    PubMed Central

    Pfoh, Roland; Pai, Emil F.; Saridakis, Vivian

    2015-01-01

    Nicotinamide mononucleotide adenylyltransferase (NMNAT) catalyzes the biosynthesis of NAD+ and NaAD+. The crystal structure of NMNAT from Methanobacterium thermoautotrophicum complexed with NAD+ and SO4 2− revealed the active-site residues involved in binding and catalysis. Site-directed mutagenesis was used to further characterize the roles played by several of these residues. Arg11 and Arg136 were implicated in binding the phosphate groups of the ATP substrate. Both of these residues were mutated to lysine individually. Arg47 does not interact with either NMN or ATP substrates directly, but was deemed to play a role in binding as it is proximal to Arg11 and Arg136. Arg47 was mutated to lysine and glutamic acid. Surprisingly, when expressed in Escherichia coli all of these NMNAT mutants trapped a molecule of NADP+ in their active sites. This NADP+ was bound in a conformation that was quite different from that displayed by NAD+ in the native enzyme complex. When NADP+ was co-crystallized with wild-type NMNAT, the same structural arrangement was observed. These studies revealed a different conformation of NADP+ in the active site of NMNAT, indicating plasticity of the active site. PMID:26457427

  16. Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    PubMed Central

    Coda, Davide M; Gaarenstroom, Tessa; East, Philip; Patel, Harshil; Miller, Daniel S J; Lobley, Anna; Matthews, Nik; Stewart, Aengus; Hill, Caroline S

    2017-01-01

    NODAL/Activin signaling orchestrates key processes during embryonic development via SMAD2. How SMAD2 activates programs of gene expression that are modulated over time however, is not known. Here we delineate the sequence of events that occur from SMAD2 binding to transcriptional activation, and the mechanisms underlying them. NODAL/Activin signaling induces dramatic chromatin landscape changes, and a dynamic transcriptional network regulated by SMAD2, acting via multiple mechanisms. Crucially we have discovered two modes of SMAD2 binding. SMAD2 can bind pre-acetylated nucleosome-depleted sites. However, it also binds to unacetylated, closed chromatin, independently of pioneer factors, where it induces nucleosome displacement and histone acetylation. For a subset of genes, this requires SMARCA4. We find that long term modulation of the transcriptional responses requires continued NODAL/Activin signaling. Thus SMAD2 binding does not linearly equate with transcriptional kinetics, and our data suggest that SMAD2 recruits multiple co-factors during sustained signaling to shape the downstream transcriptional program. DOI: http://dx.doi.org/10.7554/eLife.22474.001 PMID:28191871

  17. Effects of driving mode on the performance of multiple-chamber piezoelectric pumps with multiple actuators

    NASA Astrophysics Data System (ADS)

    Zhang, Zhonghua; Kan, Junwu; Wang, Shuyun; Wang, Hongyun; Ma, Jijie; Jiang, Yonghua

    2015-09-01

    Due to the limited output capability of piezoelectric diaphragm pumps, the driving voltage is frequently increased to obtain the desired output. However, the excessive voltage application may lead to a large deformation in the piezoelectric ceramics, which could cause it to breakdown or become damaged. Therefore, increasing the number of chambers to obtain the desired output is proposed. Using a check-valve quintuple-chamber pump with quintuple piezoelectric actuators, the characteristics of the pump under different driving modes are investigated through experiments. By changing the number and connection mode of working actuators, pump performances in terms of flow rate and backpressure are tested at a voltage of 150 V with a frequency range of 60 Hz -400 Hz. Experiment results indicate that the properties of the multiple-chamber pump change significantly with distinct working chambers even though the number of pumping chambers is the same. Pump performance declines as the distance between the working actuators increases. Moreover, pump performance declines dramatically when the working piezoelectric actuator closest to the outlet is involved. The maximum backpressures of the pump with triple, quadruple, and quintuple actuators are increased by 39%, 83%, and 128%, respectively, compared with the pump with double working actuators; the corresponding maximum flow rates of the pumps are simply increased by 25.9%, 49.2%, and 67.8%, respectively. The proposed research offers practical guidance for the effective utilization of the multiple-chamber pumps under different driving modes.

  18. Comparison and correlation of binding mode of ATP in the kinase domains of Hexokinase family

    PubMed Central

    Kumar, Yellapu Nanda; Kumar, Pasupuleti Santhosh; Sowjenya, Gopal; Rao, Valasani Koteswara; Yeswanth, Sthanikam; Prasad, Uppu Venkateswara; Pradeepkiran, Jangampalli Adi; Sarma, PVGK; Bhaskar, Matcha

    2012-01-01

    Hexokinases (HKs) are the enzymes that catalyses the ATP dependent phosphorylation of Hexose sugars to Hexose-6-Phosphate (Hex-6-P). There exist four different forms of HKs namely HK-I, HK-II, HK-III and HK-IV and all of them share a common ATP binding site core surrounded by more variable sequence that determine substrate affinities. Although they share a common binding site but they differ in their kinetic functions, hence the present study is aimed to analyze the binding mode of ATP. The analysis revealed that the four ATP binding domains are showing 13 identical, 7 similar and 6 dissimilar residues with similar structural conformation. Molecular docking of ATP into the kinase domains using Molecular Operating Environment (MOE) soft ware tool clearly showed the variation in the binding mode of ATP with variable docking scores. This probably explains the variable phosphorylation rates among hexokinases family. PMID:22829728

  19. Determination of the drug-DNA binding modes using fluorescence-based assays.

    PubMed

    Williams, Alicia K; Dasilva, Sofia Cheliout; Bhatta, Ankit; Rawal, Baibhav; Liu, Melinda; Korobkova, Ekaterina A

    2012-03-15

    Therapeutic drugs and environmental pollutants may exhibit high reactivity toward DNA bases and backbone. Understanding the mechanisms of drug-DNA binding is crucial for predicting their potential genotoxicity. We developed a fluorescence analytical method for the determination of the preferential binding mode for drug-DNA interactions. Two nucleic acid dyes were employed in the method: TO-PRO-3 iodide (TP3) and 4',6-diamidino-2-phenylindole (DAPI). TP3 binds DNA by intercalation, whereas DAPI exhibits minor groove binding. Both dyes exhibit significant fluorescence magnification on binding to DNA. We evaluated the DNA binding constant, K(b), for each dye. We also performed fluorescence quenching experiments with 11 molecules of various structures and measured a C(50) value for each compound. We determined preferential binding modes for the aforementioned molecules and found that they bound to DNA consistently, as indicated by other studies. The values of the likelihood of DNA intercalation were correlated with the partition coefficients of the molecules. In addition, we performed nuclear magnetic resonance (NMR) studies of the interactions with calf thymus DNA for the three molecules. The results were consistent with the fluorescence method described above. Thus, we conclude that the fluorescence method we developed provides a reliable determination of the likelihoods of the two different DNA binding modes.

  20. High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding.

    PubMed

    Zuo, Zheng; Stormo, Gary D

    2014-11-01

    Knowing the specificity of transcription factors is critical to understanding regulatory networks in cells. The lac repressor-operator system has been studied for many years, but not with high-throughput methods capable of determining specificity comprehensively. Details of its binding interaction and its selection of an asymmetric binding site have been controversial. We employed a new method to accurately determine relative binding affinities to thousands of sequences simultaneously, requiring only sequencing of bound and unbound fractions. An analysis of 2560 different DNA sequence variants, including both base changes and variations in operator length, provides a detailed view of lac repressor sequence specificity. We find that the protein can bind with nearly equal affinities to operators of three different lengths, but the sequence preference changes depending on the length, demonstrating alternative modes of interaction between the protein and DNA. The wild-type operator has an odd length, causing the two monomers to bind in alternative modes, making the asymmetric operator the preferred binding site. We tested two other members of the LacI/GalR protein family and find that neither can bind with high affinity to sites with alternative lengths or shows evidence of alternative binding modes. A further comparison with known and predicted motifs suggests that the lac repressor may be unique in this ability and that this may contribute to its selection.

  1. Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage.

    PubMed

    Lavoie, Mathieu; Abou Elela, Sherif

    2008-08-19

    Members of the bacterial RNase III family recognize a variety of short structured RNAs with few common features. It is not clear how this group of enzymes supports high cleavage fidelity while maintaining a broad base of substrates. Here we show that the yeast orthologue of RNase III (Rnt1p) uses a network of 2'-OH-dependent interactions to recognize substrates with different structures. We designed a series of bipartite substrates permitting the distinction between binding and cleavage defects. Each substrate was engineered to carry a single or multiple 2'- O-methyl or 2'-fluoro ribonucleotide substitutions to prevent the formation of hydrogen bonds with a specific nucleotide or group of nucleotides. Interestingly, introduction of 2'- O-methyl ribonucleotides near the cleavage site increased the rate of catalysis, indicating that 2'-OH are not required for cleavage. Substitution of nucleotides in known Rnt1p binding site with 2'- O-methyl ribonucleotides inhibited cleavage while single 2'-fluoro ribonucleotide substitutions did not. This indicates that while no single 2'-OH is essential for Rnt1p cleavage, small changes in the substrate structure are not tolerated. Strikingly, several nucleotide substitutions greatly increased the substrate dissociation constant with little or no effect on the Michaelis-Menten constant or rate of catalysis. Together, the results indicate that Rnt1p uses a network of nucleotide interactions to identify its substrate and support two distinct modes of binding. One mode is primarily mediated by the dsRNA binding domain and leads to the formation of stable RNA/protein complex, while the other requires the presence of the nuclease and N-terminal domains and leads to RNA cleavage.

  2. A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings

    NASA Astrophysics Data System (ADS)

    Chen, Jianzhong; Wang, Jinan; Zhu, Weiliang; Li, Guohui

    2013-11-01

    Molecular dynamics (MD) simulations followed by principal component analysis were performed to study the conformational change of MDM2 induced by p53 and two inhibitor (P4 and MI63a) bindings. The results show that the hydrophobic cleft of MDM2 is very flexible and adaptive to different structural binding partners. The cleft tends to become wider and more stable as MDM2 binds to the three binding partners, while unbound MDM2 shows a narrower and pretty flexible cleft, which agrees with recent experimental data and theoretical studies. It was also found that the binding of P4 and p53 stabilizes the motion of the loop L2 linking the helix α2 and β strand (β3), but the presence of MI63a makes the motion of L2 disordered. In addition, the binding free energies of the three partners to MDM2 were calculated using molecular mechanics generalized Born surface area to explain the binding modes of these three partners to MDM2. This study will be helpful not only for better understanding the functional, concerted motion of MDM2, but also for the rational design of potent anticancer drugs targeting the p53-MDM2 interaction.

  3. Prediction of the binding mode of N2-phenylguanine derivative inhibitors to herpes simplex virus type 1 thymidine kinase

    NASA Astrophysics Data System (ADS)

    Gaudio, Anderson Coser; Takahata, Yuji; Richards, William Graham

    1998-01-01

    The probable binding mode of the herpes simplex virus thymidine kinase (HSV1 TK) N2-[substituted]-phenylguanine inhibitors is proposed. A computational experiment was designed to check some qualitative binding parameters and to calculate the interaction binding energies of alternative binding modes of N2-phenylguanines. The known binding modes of the HSV1 TK natural substrate deoxythymidine and one of its competitive inhibitors ganciclovir were used as templates. Both the qualitative and quantitative parts of the computational experiment indicated that the N2-phenylguanine derivatives bind to the HSV1 TK active site in the deoxythymidine-like binding mode. An experimental observation that N2-phenylguanosine derivatives are not phosphorylated during the interaction with the HSV1 TK gives support to the proposed binding mode.

  4. Real-time multi-mode neutron multiplicity counter

    DOEpatents

    Rowland, Mark S; Alvarez, Raymond A

    2013-02-26

    Embodiments are directed to a digital data acquisition method that collects data regarding nuclear fission at high rates and performs real-time preprocessing of large volumes of data into directly useable forms for use in a system that performs non-destructive assaying of nuclear material and assemblies for mass and multiplication of special nuclear material (SNM). Pulses from a multi-detector array are fed in parallel to individual inputs that are tied to individual bits in a digital word. Data is collected by loading a word at the individual bit level in parallel, to reduce the latency associated with current shift-register systems. The word is read at regular intervals, all bits simultaneously, with no manipulation. The word is passed to a number of storage locations for subsequent processing, thereby removing the front-end problem of pulse pileup. The word is used simultaneously in several internal processing schemes that assemble the data in a number of more directly useable forms. The detector includes a multi-mode counter that executes a number of different count algorithms in parallel to determine different attributes of the count data.

  5. Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists

    PubMed Central

    Barron, Mace G.

    2017-01-01

    The flexible hydrophobic ligand binding pocket (LBP) of estrogen receptor α (ERα) allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D) protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicable to other nuclear receptors. PMID:28061508

  6. Binding Mode Selection Determines the Action of Ecstasy Homologs at Monoamine Transporters

    PubMed Central

    Sandtner, Walter; Stockner, Thomas; Hasenhuetl, Peter S.; Partilla, John S.; Seddik, Amir; Zhang, Yuan-Wei; Cao, Jianjing; Holy, Marion; Steinkellner, Thomas; Rudnick, Gary; Baumann, Michael H.; Ecker, Gerhard F.; Newman, Amy Hauck

    2016-01-01

    Determining the structural elements that define substrates and inhibitors at the monoamine transporters is critical to elucidating the mechanisms underlying these disparate functions. In this study, we addressed this question directly by generating a series of N-substituted 3,4-methylenedioxyamphetamine analogs that differ only in the number of methyl substituents on the terminal amine group. Starting with 3,4-methylenedioxy-N-methylamphetamine, 3,4-methylenedioxy-N,N-dimethylamphetamine (MDDMA) and 3,4-methylenedioxy-N,N,N-trimethylamphetamine (MDTMA) were prepared. We evaluated the functional activities of the compounds at all three monoamine transporters in native brain tissue and cells expressing the transporters. In addition, we used ligand docking to generate models of the respective protein-ligand complexes, which allowed us to relate the experimental findings to available structural information. Our results suggest that the 3,4-methylenedioxyamphetamine analogs bind at the monoamine transporter orthosteric binding site by adopting one of two mutually exclusive binding modes. 3,4-methylenedioxyamphetamine and 3,4-methylenedioxy-N-methylamphetamine adopt a high-affinity binding mode consistent with a transportable substrate, whereas MDDMA and MDTMA adopt a low-affinity binding mode consistent with an inhibitor, in which the ligand orientation is inverted. Importantly, MDDMA can alternate between both binding modes, whereas MDTMA exclusively binds to the low-affinity mode. Our experimental results are consistent with the idea that the initial orientation of bound ligands is critical for subsequent interactions that lead to transporter conformational changes and substrate translocation. PMID:26519222

  7. Insight into the Binding Mode of Agonists of the Nicotinic Acetylcholine Receptor from Calculated Electron Densities

    PubMed Central

    Beck, Michael E; Gutbrod, Oliver; Matthiesen, Svend

    2015-01-01

    Insect nicotinic acetylcholine receptors (nAChRs) are among the most prominent and most economically important insecticide targets. Thus, an understanding of the modes of binding of respective agonists is important for the design of specific compounds with favorable vertebrate profiles. In the case of nAChRs, the lack of available high-resolution X-ray structures leaves theoretical considerations as the only viable option. Starting from classical homology and docking approaches, binding mode hypotheses are created for five agonists of the nAChR, covering insecticides in the main group 4 of the Insecticide Resistance Action Committee (IRAC) mode of action (MoA) classification, namely, neonicotinoids, nicotine, sulfoxaflor, and butenolides. To better understand these binding modes, the topologies of calculated electron densities of small-model systems are analyzed in the framework of the quantum theory of atoms in molecules. The theoretically obtained modes of binding are very much in line with the biology-driven IRAC MoA classification of the investigated ligands. PMID:26175091

  8. Insight into the Binding Mode of Agonists of the Nicotinic Acetylcholine Receptor from Calculated Electron Densities.

    PubMed

    Beck, Michael E; Gutbrod, Oliver; Matthiesen, Svend

    2015-07-15

    Insect nicotinic acetylcholine receptors (nAChRs) are among the most prominent and most economically important insecticide targets. Thus, an understanding of the modes of binding of respective agonists is important for the design of specific compounds with favorable vertebrate profiles. In the case of nAChRs, the lack of available high-resolution X-ray structures leaves theoretical considerations as the only viable option. Starting from classical homology and docking approaches, binding mode hypotheses are created for five agonists of the nAChR, covering insecticides in the main group 4 of the Insecticide Resistance Action Committee (IRAC) mode of action (MoA) classification, namely, neonicotinoids, nicotine, sulfoxaflor, and butenolides. To better understand these binding modes, the topologies of calculated electron densities of small-model systems are analyzed in the framework of the quantum theory of atoms in molecules. The theoretically obtained modes of binding are very much in line with the biology-driven IRAC MoA classification of the investigated ligands.

  9. Rigorous Treatment of Multi-species Multi-mode Ligand-Receptor Interactions in 3D-QSAR: CoMFA Analysis of Thyroxine Analogs Binding to Transthyretin

    PubMed Central

    Natesan, Senthil; Wang, Tiansheng; Lukacova, Viera; Bartus, Vladimir; Khandelwal, Akash; Balaz, Stefan

    2011-01-01

    For a rigorous analysis of the receptor-ligand binding, speciation of the ligands caused by ionization, tautomerism, covalent hydration, and dynamic stereoisomerism needs to be considered. Each species may bind in several orientations or conformations (modes), especially for flexible ligands and receptors. A thermodynamic description of the multi-species (MS), multi-mode (MM) binding events shows that the overall association constant is equal to the weighted sum of the sums of microscopic association constants of individual modes for each species, with the weights given by the unbound fractions of individual species. This expression is a prerequisite for a precise quantitative characterization of the ligand-receptor interactions in both structure-based and ligand-based structure-activity analyses. We have implemented the MS-MM correlation expression into the Comparative Molecular Field Analysis (CoMFA), which deduces a map of the binding site from structures and binding affinities of a ligand set, in the absence of experimental structural information on the receptor. The MS-MM CoMFA approach was applied to published data for binding to transthyretin of 28 thyroxine analogs, each forming up to four ionization species under physiological conditions. The published X-ray structures of several analogs, exhibiting multiple binding modes, served as templates for the MS-MM superposition of thyroxine analogs. Additional modes were generated for compounds with flexible alkyl substituents, to identify bound conformations. The results demonstrate that the MS-MM modification improved predictive abilities of the CoMFA models, even for the standard procedure with MS-MM selected species and modes. The predicted prevalences of individual modes and the generated receptor site model are in reasonable agreement with the available X-ray data. The calibrated model can help in the design of inhibitors of transthyretin amyloid fibril formation. PMID:21476521

  10. Mode of binding of the antithyroid drug propylthiouracil to mammalian haem peroxidases

    PubMed Central

    Singh, R. P.; Singh, A.; Kushwaha, G. S; Singh, A. K.; Kaur, P.; Sharma, S.; Singh, T. P.

    2015-01-01

    The mammalian haem peroxidase superfamily consists of myeloperoxidase (MPO), lactoperoxidase (LPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). These enzymes catalyze a number of oxidative reactions of inorganic substrates such as Cl−, Br−, I− and SCN− as well as of various organic aromatic compounds. To date, only structures of MPO and LPO are known. The substrate-binding sites in these enzymes are located on the distal haem side. Propylthiouracil (PTU) is a potent antithyroid drug that acts by inhibiting the function of TPO. It has also been shown to inhibit the action of LPO. However, its mode of binding to mammalian haem peroxidases is not yet known. In order to determine the mode of its binding to peroxidases, the structure of the complex of LPO with PTU has been determined. It showed that PTU binds to LPO in the substrate-binding site on the distal haem side. The IC50 values for the inhibition of LPO and TPO by PTU are 47 and 30 µM, respectively. A comparision of the residues surrounding the substrate-binding site on the distal haem side in LPO with those in TPO showed that all of the residues were identical except for Ala114 (LPO numbering scheme), which is replaced by Thr205 (TPO numbering scheme) in TPO. A threonine residue in place of alanine in the substrate-binding site may affect the affinity of PTU for peroxidases. PMID:25760705

  11. THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions.

    PubMed

    Woods, K N

    2014-03-01

    Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster large-scale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG)3. These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG)3. Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α- and β- domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.

  12. 78 FR 52970 - Certain Multiple Mode Outdoor Grills and Parts Thereof; Notice of Receipt of Complaint...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-27

    ... COMMISSION Certain Multiple Mode Outdoor Grills and Parts Thereof; Notice of Receipt of Complaint... complaint entitled Certain Multiple Mode Outdoor Grills and Parts Thereof, DN 2974; the Commission is... can be accessed on the Commission's Electronic Document Information System (EDIS) at EDIS \\1\\,...

  13. The binding modes of carbazole derivatives with telomere G-quadruplex

    NASA Astrophysics Data System (ADS)

    Zhang, Xiu-feng; Zhang, Hui-juan; Xiang, Jun-feng; Li, Qian; Yang, Qian-fan; Shang, Qian; Zhang, Yan-xia; Tang, Ya-lin

    2010-10-01

    It is reported that carbazole derivatives can stabilize G-quadruplex DNA structure formed by human telomeric sequence, and therefore, they have the potential to serve as anti-cancer agents. In this present study, in order to further explore the binding mode between carbazole derivatives and G-quadruplex formed by human telomeric sequence, two carbazole iodides (BMVEC, MVEC) molecules were synthesized and used to investigate the interaction with the human telomeric parallel and antiparallel G-quadruplex structures by NMR, CD and molecular modeling study. Interestingly, it is the pivotal the cationic charge pendant groups of pyridinium rings of carbazole that plays an essential role in the stabilizing and binding mode of the human telomeric sequences G-quadruplex structure. It was found that BMVEC with two cationic charge pendant groups of pyridinium rings of 9-ethylcarbazole cannot only stabilize parallel G-quadruple of Hum6 by groove binding and G-tetrad stacking modes and antiparallel G-quadruplex of Hum22 by groove binding, but also induce the formation of mixed G-quadruplex of Hum22. While MVEC with one cationic charge pendant groups of pyridinium ring only can bind with the parallel G-quadruplex of Hum6 by the stacking onto the G4 G-tetrad and could not interact with the G-quadruplex of Hum22.

  14. DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes.

    PubMed

    Reis, L A; Rocha, M S

    2017-05-01

    In this work, we use force spectroscopy to investigate the interaction between the DAPI fluorescent dye and the λ-DNA molecule under high (174 mM) and low (34 mM) ionic strengths. Firstly, we have measured the changes on the mechanical properties (persistence and contour lengths) of the DNA-DAPI complexes as a function of the dye concentration in the sample. Then, we use recently developed models in order to connect the behavior of both mechanical properties to the physical chemistry of the interaction. Such analysis has allowed us to identify and to decouple two main binding modes, determining the relevant physicochemical (binding) parameters for each of these modes: minor groove binding, which saturates at very low DAPI concentrations ( CT ∼ 0.50 μM) and presents equilibrium binding constants of the order of ∼10(7) M(-1) for the two ionic strengths studied; and intercalation, which starts to play a significant role only after the saturation of the first mode, presenting much smaller equilibrium binding constants (∼10(5) M(-1) ).

  15. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

    SciTech Connect

    Wong, Jaslyn E. M. M.; Midtgaard, Søren Roi; Gysel, Kira; Thygesen, Mikkel B.; Sørensen, Kasper K.; Jensen, Knud J.; Stougaard, Jens; Thirup, Søren; Blaise, Mickaël

    2015-03-01

    The crystal and solution structures of the T. thermophilus NlpC/P60 d, l-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan. LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed.

  16. Multiple relaxation modes in associative polymer networks with varying connectivity

    NASA Astrophysics Data System (ADS)

    Bohdan, M.; Sprakel, J.; van der Gucht, J.

    2016-09-01

    The dynamics and mechanics of networks depend sensitively on their spatial connectivity. To explore the effect of connectivity on local network dynamics, we prepare transient polymer networks in which we systematically cut connecting bonds. We do this by creating networks formed from hydrophobically modified difunctionalized polyethylene glycol chains. These form physical gels, consisting of flowerlike micelles that are transiently cross-linked by connecting bridges. By introducing monofunctionalized chains, we can systematically reduce the number of bonds between micelles and thus lower the network connectivity, which strongly reduces the network elasticity and relaxation time. Dynamic light scattering reveals a complex relaxation dynamics that are not apparent in bulk rheology. We observe three distinct relaxation modes. First we find a fast diffusive mode that does not depend on the number of bridges and is attributed to the diffusion of micelles within a cage formed by neighboring micelles. A second, intermediate mode depends strongly on network connectivity but surprisingly is independent of the scattering vector q . We attribute this viscoelastic mode to fluctuations in local connectivity of the network. The third, slowest mode is also diffusive and is attributed to the diffusion of micelle clusters through the viscoelastic matrix. These results shed light on the microscopic dynamics in weakly interconnected transient networks.

  17. The Multiple Carbohydrate Binding Specificities of Helicobacter pylori

    NASA Astrophysics Data System (ADS)

    Teneberg, Susann

    Persistent colonization of the human stomach by Helicobacter pylori is a risk factor for the development of peptic ulcer disease and gastric cancer. Adhesion of microbes to the target tissue is an important determinant for successful initiation, establishment and maintenance of infection, and a variety of different candidate carbohydrate receptors for H. pylori have been identified. Here the different the binding specifities, and their potential role in adhesion to human gastric epithelium are described. Finally, recent findings on the roles of sialic acid binding SabA adhesin in interactions with human neutrophils and erythrocytes are discussed.

  18. Azimuthal Directivity of Fan Tones Containing Multiple Modes

    NASA Technical Reports Server (NTRS)

    Heidelberg, Laurence J.; Sutliff, Daniel L.; Nallasamy, M.

    1997-01-01

    The directivity of fan tone noise is generally measured and plotted in the sideline or flyover plane and it is assumed that this curve is the same for all azimuthal angles. When two or more circumferential (m-order) modes of the same tone are present in the fan duct, an interference pattern develops in the azimuthal direction both in the duct and in the farfield. In this investigation two m-order modes of similar power were generated in a large low speed fan. Farfield measurements and a finite element propagation code both show substantial variations in the azimuthal direction. Induct mode measurement were made and used as input to the code. Although these tests may represent a worst case scenario, the validity of the current practice of assuming axisymmetry should be questioned.

  19. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants

    NASA Technical Reports Server (NTRS)

    Yang, Tianbao; Poovaiah, B. W.

    2002-01-01

    We reported earlier that the tobacco early ethylene-responsive gene NtER1 encodes a calmodulin-binding protein (Yang, T., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 38467-38473). Here we demonstrate that there is one NtER1 homolog as well as five related genes in Arabidopsis. These six genes are rapidly and differentially induced by environmental signals such as temperature extremes, UVB, salt, and wounding; hormones such as ethylene and abscisic acid; and signal molecules such as methyl jasmonate, H(2)O(2), and salicylic acid. Hence, they were designated as AtSR1-6 (Arabidopsis thaliana signal-responsive genes). Ca(2+)/calmodulin binds to all AtSRs, and their calmodulin-binding regions are located on a conserved basic amphiphilic alpha-helical motif in the C terminus. AtSR1 targets the nucleus and specifically recognizes a novel 6-bp CGCG box (A/C/G)CGCG(G/T/C). The multiple CGCG cis-elements are found in promoters of genes such as those involved in ethylene signaling, abscisic acid signaling, and light signal perception. The DNA-binding domain in AtSR1 is located on the N-terminal 146 bp where all AtSR1-related proteins share high similarity but have no similarity to other known DNA-binding proteins. The calmodulin-binding nuclear proteins isolated from wounded leaves exhibit specific CGCG box DNA binding activities. These results suggest that the AtSR gene family encodes a family of calmodulin-binding/DNA-binding proteins involved in multiple signal transduction pathways in plants.

  20. Theoretical prediction of binding modes and hot sequences for allopsoralen DNA interaction

    NASA Astrophysics Data System (ADS)

    Méndez, Patricia Saenz; Guedes, Rita C.; dos Santos, Daniel J. V. A.; Eriksson, Leif A.

    2007-12-01

    Molecular docking studies of two duplex DNA sequences as target fragments and allopsoralen as ligand were performed. The calculated interaction energies showed that the ligand can be docked into the minor groove as well as become intercalated. However, unlike psoralen, allopsoralen preferred binding mode for non-poly-TA sequences is minor groove binding. Calculated energies for intercalation between different base pairs suggest that the predicted sequence selectivity for allopsoralen is analogous to that observed for psoralen. Intercalation is favored in 5'-TpA sites in poly-TA sequences.

  1. Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA

    NASA Astrophysics Data System (ADS)

    Tao, Mo; Zhang, Guowen; Pan, Junhui; Xiong, Chunhong

    2016-02-01

    Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 104 L mol- 1, and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.

  2. Binding modes of thioflavin T molecules to prion peptide assemblies identified by using scanning tunneling microscopy.

    PubMed

    Mao, Xiaobo; Guo, Yuanyuan; Wang, Chenxuan; Zhang, Min; Ma, Xiaojing; Liu, Lei; Niu, Lin; Zeng, Qingdao; Yang, Yanlian; Wang, Chen

    2011-06-15

    The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.

  3. Multiple approaches to assess pectin binding to galectin-3.

    PubMed

    Zhang, Tao; Zheng, Yi; Zhao, Dongyang; Yan, Jingmin; Sun, Chongliang; Zhou, Yifa; Tai, Guihua

    2016-10-01

    Although several approaches have been used to evaluate binding of carbohydrates to lectins, results are not always comparable, especially with larger polysaccharides. Here, we quantitatively assessed and compared binding of pectin-derived polysaccharides to galectin-3 (Gal-3) using five methods: surface plasmon resonance (SPR), bio-layer interferometry (BLI), fluorescence polarization (FP), competitive fluorescence-linked immunosorbance (cFLISA), and the well-known cell-based hemagglutination assay (G3H). Our studies revealed that whereas Gal-3-pectin binding parameters determined by SPR and BLI were comparable and correlated with inhibitory potencies from the G3H assay, results using FP and cFLISA assays were highly variable and depended greatly on the probe and mass of the polysaccharide. In the cFLISA assay, for example, pectins showed no inhibition when using the DTAF-labeled asialofetuin probe, but did when using a DTAF-labeled pectin probe. And the FP approach with the DTAF-lactose probe did not work on polysaccharides and large galactan chains, although it did work well with smaller galactans. Nevertheless, even though results derived from all of these methods are in general agreement, derived KD, IC50, and MIC values do differ. Our results reflect the variability using various techniques and therefore will be useful to investigators who are developing pectin-derived Gal-3 antagonists as anti-cancer agents.

  4. Pulsed squeezed light: Simultaneous squeezing of multiple modes

    SciTech Connect

    Wasilewski, Wojciech; Lvovsky, A. I.; Banaszek, Konrad; Radzewicz, Czeslaw

    2006-06-15

    We analyze the spectral properties of squeezed light produced by means of pulsed, single-pass degenerate parametric down-conversion. The multimode output of this process can be decomposed into characteristic modes undergoing independent squeezing evolution akin to the Schmidt decomposition of the biphoton spectrum. The main features of this decomposition can be understood using a simple analytical model developed in the perturbative regime. In the strong pumping regime, for which the perturbative approach is not valid, we present a numerical analysis, specializing to the case of one-dimensional propagation in a beta-barium borate waveguide. Characterization of the squeezing modes provides us with an insight necessary for optimizing homodyne detection of squeezing. For a weak parametric process, efficient squeezing is found in a broad range of local oscillator modes, whereas the intense generation regime places much more stringent conditions on the local oscillator. We point out that without meeting these conditions, the detected squeezing can actually diminish with the increasing pumping strength, and we expose physical reasons behind this inefficiency.

  5. 2,4-Diaminopyrimidine MK2 inhibitors. Part I: Observation of an unexpected inhibitor binding mode

    SciTech Connect

    Argiriadi, Maria A.; Ericsson, Anna M.; Harris, Christopher M.; Banach, David L.; Borhani, David W.; Calderwood, David J.; Demers, Megan D.; DiMauro, Jennifer; Dixon, Richard W.; Hardman, Jennifer; Kwak, Silvia; Li, Biqin; Mankovich, John A.; Marcotte, Douglas; Mullen, Kelly D.; Ni, Baofu; Pietras, M.; Sadhukhan, Ramkrishna; Sousa, Silvino; Tomlinson, Medha J.; Wang, L.; Xiang, T.; Talanian, R.V.

    2010-09-17

    MK2 is a Ser/Thr kinase of significant interest as an anti-inflammatory drug discovery target. Here we describe the development of in vitro tools for the identification and characterization of MK2 inhibitors, including validation of inhibitor interactions with the crystallography construct and determination of the unique binding mode of 2,4-diaminopyrimidine inhibitors in the MK2 active site.

  6. Comprehensive 3D-QSAR and binding mode of BACE-1 inhibitors using R-group search and molecular docking.

    PubMed

    Huang, Dandan; Liu, Yonglan; Shi, Bozhi; Li, Yueting; Wang, Guixue; Liang, Guizhao

    2013-09-01

    The β-enzyme (BACE), which takes an active part in the processing of amyloid precursor protein, thereby leads to the production of amyloid-β (Aβ) in the brain, is a major therapeutic target against Alzheimer's disease. The present study is aimed at studying 3D-QSAR of BACE-1 inhibitors and their binding mode. We build a 3D-QSAR model involving 99 training BACE-1 inhibitors based on Topomer CoMFA, and 26 molecules are employed to validate the external predictive power of the model obtained. The multiple correlation coefficients of fitting modeling, leave one out cross validation, and external validation are 0.966, 0.767 and 0.784, respectively. Topomer search is used as a tool for virtual screening in lead-like compounds of ZINC databases (2012); as a result, we successfully design 30 new molecules with higher activity than that of all training and test inhibitors. Besides, Surflex-dock is employed to explore binding mode of the inhibitors studied when acting with BACE-1 enzyme. The result shows that the inhibitors closely interact with the key sites related to ASP93, THR133, GLN134, ASP289, GLY291, THR292, THR293, ASN294, ARG296 and SER386 of BACE-1.

  7. Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors

    PubMed Central

    2016-01-01

    Available crystal structures of opioid receptors provide a high-resolution picture of ligand binding at the primary (“orthosteric”) site, that is, the site targeted by endogenous ligands. Recently, positive allosteric modulators of opioid receptors have also been discovered, but their modes of binding and action remain unknown. Here, we use a metadynamics-based strategy to efficiently sample the binding process of a recently discovered positive allosteric modulator of the δ-opioid receptor, BMS-986187, in the presence of the orthosteric agonist SNC-80, and with the receptor embedded in an explicit lipid–water environment. The dynamics of BMS-986187 were enhanced by biasing the potential acting on the ligand–receptor distance and ligand–receptor interaction contacts. Representative lowest-energy structures from the reconstructed free-energy landscape revealed two alternative ligand binding poses at an allosteric site delineated by transmembrane (TM) helices TM1, TM2, and TM7, with some participation of TM6. Mutations of amino acid residues at these proposed allosteric sites were found to either affect the binding of BMS-986187 or its ability to modulate the affinity and/or efficacy of SNC-80. Taken together, these combined experimental and computational studies provide the first atomic-level insight into the modulation of opioid receptor binding and signaling by allosteric modulators. PMID:26841170

  8. Computational determination of the binding mode of α-conotoxin to nicotinic acetylcholine receptor

    NASA Astrophysics Data System (ADS)

    Tabassum, Nargis; Yu, Rilei; Jiang, Tao

    2016-12-01

    Conotoxins belong to the large families of disulfide-rich peptide toxins from cone snail venom, and can act on a broad spectrum of ion channels and receptors. They are classified into different subtypes based on their targets. The α-conotoxins selectively inhibit the current of the nicotinic acetylcholine receptors. Because of their unique selectivity towards distinct nAChR subtypes, α-conotoxins become valuable tools in nAChR study. In addition to the X-ray structures of α-conotoxins in complex with acetylcholine-binding protein, a homolog of the nAChR ligand-binding domain, the high-resolution crystal structures of the extracellular domain of the α1 and α9 subunits are also obtained. Such structures not only revealed the details of the configuration of nAChR, but also provided higher sequence identity templates for modeling the binding modes of α-conotoxins to nAChR. This mini-review summarizes recent modeling studies for the determination of the binding modes of α-conotoxins to nAChR. As there are not crystal structures of the nAChR in complex with conotoxins, computational modeling in combination of mutagenesis data is expected to reveal the molecular recognition mechanisms that govern the interactions between α-conotoxins and nAChR at molecular level. An accurate determination of the binding modes of α-conotoxins on AChRs allows rational design of α-conotoxin analogues with improved potency or selectivity to nAChRs.

  9. Change of the binding mode of the DNA/proflavine system induced by ethanol.

    PubMed

    García, Begoña; Leal, José M; Ruiz, Rebeca; Biver, Tarita; Secco, Fernando; Venturini, M

    2010-07-01

    The equilibria and kinetics of the binding of proflavine to poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) were investigated in ethanol/water mixtures using spectrophotometric, circular dichroism, viscometric, and T-jump methods. All methods concur in showing that two modes of interaction are operative: intercalation and surface binding. The latter mode is favored by increasing ethanol and/or the proflavine content. Both static and kinetic experiments show that, concerning the poly(dG-dC).poly(dG-dC)/proflavine system, intercalation largely prevails up to 20% EtOH. For higher EtOH levels surface binding becomes dominant. Concerning the poly(dA-dT).poly(dA-dT)/proflavine system, melting experiments show that addition of proflavine stabilizes the double stranded structure, but the effect is reduced in the presence of EtOH. The DeltaH degrees and DeltaS degrees values of the melting process, measured at different concentrations of added proflavine, are linearly correlated, revealing the presence of the enthalpy-entropy compensation phenomenon (EEC). The nonmonotonicity of the "entropic term" of the EEC reveals the transition between the two binding modes. T-jump experiments show two relaxation effects, but at the highest levels of EtOH (>25%) the kinetic curves become monophasic, confirming the prevalence of the surface complex. A branched mechanism is proposed where diffusion controlled formation of a precursor complex occurs in the early stage of the binding process. This evolves toward the surface and/or the intercalated complex according to two rate-determining parallel steps. CD spectra suggest that, in the surface complex, proflavine is bound to DNA in the form of an aggregate.

  10. Distinct binding mode of multikinase inhibitor lenvatinib revealed by biochemical characterization.

    PubMed

    Okamoto, Kiyoshi; Ikemori-Kawada, Megumi; Jestel, Anja; von König, Konstanze; Funahashi, Yasuhiro; Matsushima, Tomohiro; Tsuruoka, Akihiko; Inoue, Atsushi; Matsui, Junji

    2015-01-08

    Lenvatinib is an oral multikinase inhibitor that selectively inhibits vascular endothelial growth factor (VEGF) receptors 1 to 3 and other proangiogenic and oncogenic pathway-related receptor tyrosine kinases. To elucidate the origin of the potency of lenvatinib in VEGF receptor 2 (VEGFR2) inhibition, we conducted a kinetic interaction analysis of lenvatinib with VEGFR2 and X-ray analysis of the crystal structure of VEGFR2-lenvatinib complexes. Kinetic analysis revealed that lenvatinib had a rapid association rate constant and a relatively slow dissociation rate constant in complex with VEGFR2. Co-crystal structure analysis demonstrated that lenvatinib binds at its ATP mimetic quinoline moiety to the ATP binding site and to the neighboring region via a cyclopropane ring, adopting an Asp-Phe-Gly (DFG)-"in" conformation. These results suggest that lenvatinib is very distinct in its binding mode of interaction compared to the several approved VEGFR2 kinase inhibitors.

  11. Interaction of coumarin with calf thymus DNA: deciphering the mode of binding by in vitro studies.

    PubMed

    Sarwar, Tarique; Rehman, Sayeed Ur; Husain, Mohammed Amir; Ishqi, Hassan Mubarak; Tabish, Mohammad

    2015-02-01

    DNA is the major target for a wide range of therapeutic substances. Thus, there has been considerable interest in the binding studies of small molecules with DNA. Interaction between small molecules and DNA provides a structural guideline in rational drug designing and in the synthesis of new and improved drugs with enhanced selective activity and greater clinical efficacy. Plant derived polyphenolic compounds have a large number of biological and pharmacological properties. Coumarin is a polyphenolic compound which has been extensively studied for its diverse pharmacological properties. However, its mode of interaction with DNA has not been elucidated. In the present study, we have attempted to ascertain the mode of binding of coumarin with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of UV-visible absorbance spectra and fluorescence spectra indicates the formation of complex between coumarin and Ct-DNA. Several other experiments such as effect of ionic strength, iodide induced quenching, competitive binding assay with ethidium bromide, acridine orange and Hoechst 33258 reflected that coumarin possibly binds to the minor groove of the Ct-DNA. These observations were further supported by CD spectral analysis, viscosity measurements, DNA melting studies and in silico molecular docking.

  12. Investigation of microwave photonic filter based on multiple longitudinal modes fiber laser source

    NASA Astrophysics Data System (ADS)

    Cao, Yuan; Li, Feng; Feng, Xinhuan; Lu, Chao; Guan, Bai-ou; Wai, P. K. A.

    2015-06-01

    We theoretically study the transfer function of a finite impulse response microwave photonic filter (FIR-MPF) system using a multi-wavelength fiber laser source by considering multiple longitudinal modes in each wavelength. The full response function with the response from longitudinal mode taps is obtained. We also discussed the influence of the longitudinal mode envelope and mode spacing on the performance of FIR-MPF. The response function of the longitudinal mode taps is fully discussed and the contribution is compared with the response of the carrier suppression factor for double sideband (DSB) modulation. The multiple longitudinal modes structure in the wavelength taps can be utilized to engineer the response of the FIR-MPF such that desirable features such as high side lode suppression ratio can be realized. The analysis provides a guideline for designing incoherent FIR-MPF systems.

  13. Concentric core optical fiber with multiple-mode signal transmission

    DOEpatents

    Muhs, J.D.

    1997-05-06

    A concentric core optical fiber provides for the simultaneous but independent transmission of signals over a single optical fiber. The concentric optical fiber is constructed of a single-mode or multimode inner optical fiber defined by a core and a cladding of a lower index of refraction than the core and an outer optical fiber defined by additional cladding concentrically disposed around the cladding and of an index of refraction lower than the first mentioned cladding whereby the latter functions as the core of the outer optical fiber. By employing such an optical fiber construction with a single-mode inner core or optical fiber, highly sensitive interferometric and stable less sensitive amplitude based sensors can be placed along the same length of a concentric core optical fiber. Also, by employing the concentric core optical fiber secure telecommunications can be achieved via the inner optical fiber since an intrusion of the concentric optical fiber will first cause a variation in the light being transmitted through the outer optical fiber and this variation of light being used to trigger a suitable alarm indicative of the intrusion. 3 figs.

  14. Concentric core optical fiber with multiple-mode signal transmission

    DOEpatents

    Muhs, Jeffrey D.

    1997-01-01

    A concentric core optical fiber provides for the simultaneous but independent transmission of signals over a single optical fiber. The concentric optical fiber is constructed of a single-mode or multimode inner optical fiber defined by a core and a cladding of a lower index of refraction than the core and an outer optical fiber defined by additional cladding concentrically disposed around the cladding and of an index of refraction lower than the first mentioned cladding whereby the latter functions as the core of the outer optical fiber. By employing such an optical fiber construction with a single-mode inner core or optical fiber, highly sensitive interferometric and stable less sensitive amplitude based sensors can be placed along the same length of a concentric core optical fiber. Also, by employing the concentric core optical fiber secure telecommunications can be achieved via the inner optical fiber since an intrusion of the concentric optical fiber will first cause a variation in the light being transmitted through the outer optical fiber and this variation of light being used to trigger a suitable alarm indicative of the intrusion.

  15. Multiple-Rayleigh-scatterer-induced mode splitting in a high-Q whispering-gallery-mode microresonator

    SciTech Connect

    Yi Xu; Xiao Yunfeng; Liu Yongchun; Li Beibei; Chen Youling; Li Yan; Gong Qihuang

    2011-02-15

    We theoretically investigate the mode-splitting phenomenon in a high-Q whispering-gallery-mode (WGM) microresonator coupled to multiple subwavelength Rayleigh scatterers. It is shown that the phase factors of the WGMs play the central role in such a system. Unlike the single-scatterer case, these phase factors in a multiscatterer system significantly influence both the modal coupling strength and the scattering-induced loss of a pair of counterpropagating WGMs. We scrutinize the condition for observing the splitting of transmission spectra. The mechanism can be used for highly sensitive biosensing, and the size of nanoparticles that can be detected is extended down to tens of nanometers.

  16. The binding mode of an E-64 analog to the active site of cathepsin B.

    PubMed

    Feng, M H; Chan, S L; Xiang, Y; Huber, C P; Lim, C

    1996-11-01

    Two binding modes of the isobutyl-NH-Eps-Leu-Pro inhibitor to cathepsin B have been proposed. Molecular docking using an empirical force field was carried out to distinguish between the two modes. The search began with manual docking, followed by random perturbations of the docking conformation and cycles of Monte Carlo minimization. Finally, molecular dynamics was carried out for the most favorable docking conformations. The present calculations predict that the isobutyl-NH-Eps-Leu-Pro inhibitor preferentially binds to the S' rather than the S subsites of cathepsin B. The S' binding mode prediction is supported by the X-ray crystal structure of cathepsin B bound to a closely related ethyl-O-Eps-Ile-Pro inhibitor, which was found to bind in the S'subsite with the C-terminal epoxy ring carbon making a covalent bond to the sulfur atom of Cys29. This agreement, in turn, validates our docking strategy. Furthermore, the calculations provide evidence that the dominant contribution to the total stabilization energy of the enzyme-inhibitor complex stems from the strong electrostatic interaction between the negatively charged C-terminal carboxylate group of the ligand and the positively charged imidazolium rings of His110 and His111. The latter are stabilized and held in an optimal orientation for interactions with the C-terminal end of the ligand through a salt bridge between the side chains of His110 and Asp22. By comparison with the crystal structure, some insight into the specificity of the epoxyldipeptide family towards cathepsin B inhibition has been extracted. Both the characteristics of the enzyme (e.g. subsite size and hydrophobicity) as well as the nature of the inhibitor influence the selectivity of an inhibitor towards an enzyme.

  17. Binding modes of zaragozic acid A to human squalene synthase and staphylococcal dehydrosqualene synthase.

    PubMed

    Liu, Chia-I; Jeng, Wen-Yih; Chang, Wei-Jung; Ko, Tzu-Ping; Wang, Andrew H-J

    2012-05-25

    Zaragozic acids (ZAs) belong to a family of fungal metabolites with nanomolar inhibitory activity toward squalene synthase (SQS). The enzyme catalyzes the committed step of sterol synthesis and has attracted attention as a potential target for antilipogenic and antiinfective therapies. Here, we have determined the structure of ZA-A complexed with human SQS. ZA-A binding induces a local conformational change in the substrate binding site, and its C-6 acyl group also extends over to the cofactor binding cavity. In addition, ZA-A effectively inhibits a homologous bacterial enzyme, dehydrosqualene synthase (CrtM), which synthesizes the precursor of staphyloxanthin in Staphylococcus aureus to cope with oxidative stress. Size reduction at Tyr(248) in CrtM further increases the ZA-A binding affinity, and it reveals a similar overall inhibitor binding mode to that of human SQS/ZA-A except for the C-6 acyl group. These structures pave the way for further improving selectivity and development of a new generation of anticholesterolemic and antimicrobial inhibitors.

  18. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Liu, Kai; Watanabe, Etsurou; Kokubo, Hironori

    2017-02-01

    The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose. Then, five independent MD simulations for each pose were performed with different initial velocities for the statistical analysis. Finally, the stabilities of ligand poses under MD were evaluated and compared with the native one from crystal structure. We found that about 94% of the native poses were maintained stable during the simulations, which suggests that MD simulations are accurate enough to judge most experimental binding poses as stable properly. Interestingly, incorrect decoy poses were maintained much less and 38-44% of decoys could be excluded just by performing equilibrium MD simulations, though 56-62% of decoys were stable. The computationally-heavy binding free energy calculation can be performed only for these survived poses.

  19. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Liu, Kai; Watanabe, Etsurou; Kokubo, Hironori

    2017-01-01

    The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose. Then, five independent MD simulations for each pose were performed with different initial velocities for the statistical analysis. Finally, the stabilities of ligand poses under MD were evaluated and compared with the native one from crystal structure. We found that about 94% of the native poses were maintained stable during the simulations, which suggests that MD simulations are accurate enough to judge most experimental binding poses as stable properly. Interestingly, incorrect decoy poses were maintained much less and 38-44% of decoys could be excluded just by performing equilibrium MD simulations, though 56-62% of decoys were stable. The computationally-heavy binding free energy calculation can be performed only for these survived poses.

  20. The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

    PubMed Central

    Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin

    2009-01-01

    We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409

  1. Mutational analysis of Mycobacterium tuberculosis lysine ɛ-aminotransferase and inhibitor co-crystal structures, reveals distinct binding modes.

    PubMed

    Tripathi, Sarvind Mani; Agarwal, Aparna; Ramachandran, Ravishankar

    Lysine ɛ-aminotransferase (LAT) converts lysine to α-aminoadipate-δ-semialdehyde in a PLP-mediated reaction. We mutated active-site T330, N328 and E243, and structurally rationalized their properties. T330A and T330S mutants cannot bind PLP and are inactive. N328A although inactive, binds to PLP. E243A retains activity, but binds α-ketoglutarate in a different conformation. We had earlier identified 2-aminomethyl piperidine derivative as a LAT inhibitor. The co-crystal structure reveals that it mimics binding of C5 substrates and exhibits two binding modes. E243, that shields R422 in the apo enzyme, exhibits conformational changes to permit the binding of the inhibitor in one of the binding modes. Structure-based analysis of bound water in the active site suggests optimization strategies for synthesis of improved inhibitors.

  2. Binding mode of dihydroquinazolinones with lysozyme and its antifungal activity against Aspergillus species.

    PubMed

    Hemalatha, K; Madhumitha, G; Ravi, Lokesh; Khanna, V Gopiesh; Al-Dhabi, Naif Abdullah; Arasu, Mariadhas Valan

    2016-08-01

    Aspergillosis is one of the infectious fungal diseases affecting mainly the immunocompromised patients. The scarcity of the antifungal targets has identified the importance of N-myristoyl transferase (NMT) in the regulation of fungal pathway. The dihydroquinazolinone molecules were designed on the basis of fragments responsible for binding with the target enzyme. The aryl halide, 1(a-g), aryl boronic acid and potassium carbonate were heated together in water and dioxane mixture to yield new CC bond formation in dihydroquinazolinone. The bis(triphenylphosphine)palladium(II) dichloride was used as catalyst for the CC bond formation. The synthesized series were screened for their in vitro antifungal activity against Aspergillus niger and Aspergillus fumigatus. The binding interactions of the active compound with lysozyme were explored using multiple spectroscopic studies. Molecular docking study of dihydroquinazolinones with the enzyme revealed the information regarding various binding forces involved in the interaction.

  3. Enhancing The Mode Conversion Efficiency In JET Plasmas With Multiple Mode Conversion Layers

    NASA Astrophysics Data System (ADS)

    Van Eester, D.; Lerche, E.; Johnson, T.; Hellsten, T.; Ongena, J.; Mayoral, M.-L.; Frigione, D.; Sozzi, C.; Calabro, G.; Lennholm, M.; Beaumont, P.; Blackman, T.; Brennan, D.; Brett, A.; Cecconello, M.; Coffey, I.; Coyne, A.; Crombe, K.; Czarnecka, A.; Felton, R.; Johnson, M. Gatu; Giroud, C.; Gorini, G.; Hellesen, C.; Jacquet, P.; Kazakov, Y.; Kiptily, V.; Knipe, S.; Krasilnikov, A.; Lin, Y.; Maslov, M.; Monakhov, I.; Noble, C.; Nocente, M.; Pangioni, L.; Proverbio, I.; Stamp, M.; Studholme, W.; Tardocchi, M.; Versloot, T. W.; Vdovin, V.; Whitehurst, A.; Wooldridge, E.; Zoita, V.

    2011-12-01

    The constructive interference effect described by Fuchs et al. [1] shows that the mode conversion and thereby the overall heating efficiency can be enhanced significantly when an integer number of fast wave wavelengths can be folded in between the high field side fast wave cutoff and the ion-ion hybrid layer(s) at which the ion Bernstein or ion cyclotron waves are excited. This effect was already experimentally identified in (3He)-D plasmas [2] and was recently tested in (3He)-H JET plasmas. The latter is an `inverted' scenario, which differs significantly from the (3He)-D scenarios since the mode-conversion layer is positioned between the low field side edge of the plasma and the ion-cyclotron layer of the minority 3He ions (whereas the order in which a wave entering the plasma from the low field side encounters these layers is inverted in a `regular' scenario), and because much lower 3He concentrations are needed to achieve the mode-conversion heating regime. The presence of small amounts of 4He and D in the discharges gave rise to an additional mode conversion layer on top of the expected one associated with 3He-H, which made the interpretation of the results more complex but also more interesting: Three different regimes could be distinguished as a function of X[3He], and the differing dynamics at the various concentrations could be traced back to the presence of these two mode conversion layers and their associated fast wave cutoffs. Whereas (1-D and 2-D) numerical modeling yields quantitative information on the RF absorptivity, recent analytical work by Kazakov [3] permits to grasp the dominant underlying wave interaction physics.

  4. Mutational mapping of the transmembrane binding site of the G-protein coupled receptor TGR5 and binding mode prediction of TGR5 agonists.

    PubMed

    Gertzen, Christoph G W; Spomer, Lina; Smits, Sander H J; Häussinger, Dieter; Keitel, Verena; Gohlke, Holger

    2015-11-02

    TGR5 (Gpbar-1, M-Bar) is a class A G-protein coupled bile acid-sensing receptor predominately expressed in brain, liver and gastrointestinal tract, and a promising drug target for the treatment of metabolic disorders. Due to the lack of a crystal structure of TGR5, the development of TGR5 agonists has been guided by ligand-based approaches so far. Three binding mode models of bile acid derivatives have been presented recently. However, they differ from one another in terms of overall orientation or with respect to the location and interactions of the cholane scaffold, or cannot explain all results from mutagenesis experiments. Here, we present an extended binding mode model based on an iterative and integrated computational and biological approach. An alignment of 68 TGR5 agonists based on this binding mode leads to a significant and good structure-based 3D QSAR model, which constitutes the most comprehensive structure-based 3D-QSAR study of TGR5 agonists undertaken so far and suggests that the binding mode model is a close representation of the "true" binding mode. The binding mode model is further substantiated in that effects predicted for eight mutations in the binding site agree with experimental analyses on the impact of these TGR5 variants on receptor activity. In the binding mode, the hydrophobic cholane scaffold of taurolithocholate orients towards the interior of the orthosteric binding site such that rings A and B are in contact with TM5 and TM6, the taurine side chain orients towards the extracellular opening of the binding site and forms a salt bridge with R79(EL1), and the 3-hydroxyl group forms hydrogen bonds with E169(5.44) and Y240(6.51). The binding mode thus differs in important aspects from the ones recently presented. These results are highly relevant for the development of novel, more potent agonists of TGR5 and should be a valuable starting point for the development of TGR5 antagonists, which could show antiproliferative effects in tumor

  5. A complement to the modern crystallographer's toolbox: caged gadolinium complexes with versatile binding modes.

    PubMed

    Stelter, Meike; Molina, Rafael; Jeudy, Sandra; Kahn, Richard; Abergel, Chantal; Hermoso, Juan A

    2014-06-01

    A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd(3+) ion into protein crystals in order to provide strong anomalous scattering for de novo phasing. The complexes contained multidentate ligand molecules with different functional groups to provide a panel of possible interactions with the protein. An exhaustive crystallographic analysis showed them to be nondisruptive to the diffraction quality of the prepared derivative crystals, and as many as 50% of the derivatives allowed the determination of accurate phases, leading to high-quality experimental electron-density maps. At least two successful derivatives were identified for all tested proteins. Structure refinement showed that the complexes bind to the protein surface or solvent-accessible cavities, involving hydrogen bonds, electrostatic and CH-π interactions, explaining their versatile binding modes. Their high phasing power, complementary binding modes and ease of use make them highly suitable as a heavy-atom screen for high-throughput de novo structure determination, in combination with the SAD method. They can also provide a reliable tool for the development of new methods such as serial femtosecond crystallography.

  6. In-silico identification of the binding mode of synthesized adamantyl derivatives inside cholinesterase enzymes

    PubMed Central

    Al-Aboudi, Amal; Al-Qawasmeh, Raed A; Shahwan, Alaa; Mahmood, Uzma; Khalid, Asaad; Ul-Haq, Zaheer

    2015-01-01

    Aim: To investigate the binding mode of synthesized adamantly derivatives inside of cholinesterase enzymes using molecular docking simulations. Methods: A series of hybrid compounds containing adamantane and hydrazide moieties was designed and synthesized. Their inhibitory activities against acetylcholinesterase (AChE) and (butyrylcholinesterase) BChE were assessed in vitro. The binding mode of the compounds inside cholinesterase enzymes was investigated using Surflex-Dock package of Sybyl7.3 software. Results: A total of 26 adamantyl derivatives were synthesized. Among them, adamantane-1-carboxylic acid hydrazide had an almost equal inhibitory activity towards both enzymes, whereas 10 other compounds exhibited moderate inhibitory activity against BChE. The molecular docking studies demonstrated that hydrophobic interactions between the compounds and their surrounding residues in the active site played predominant roles, while hydrophilic interactions were also found. When the compounds were docked inside each enzyme, they exhibited stronger interactions with BChE over AChE, possibly due to the larger active site of BChE. The binding affinities of the compounds for BChE and AChE estimated were in agreement with the experimental data. Conclusion: The new adamantly derivatives selectively inhibit BChE with respect to AChE, thus making them good candidates for testing the hypothesis that BChE inhibitors would be more efficient and better tolerated than AChE inhibitors in the treatment of Alzheimer's disease. PMID:25937631

  7. Understanding TRPV1 activation by ligands: Insights from the binding modes of capsaicin and resiniferatoxin

    PubMed Central

    Elokely, Khaled; Velisetty, Phanindra; Delemotte, Lucie; Palovcak, Eugene; Klein, Michael L.; Rohacs, Tibor; Carnevale, Vincenzo

    2016-01-01

    The transient receptor potential cation channel subfamily V member 1 (TRPV1) or vanilloid receptor 1 is a nonselective cation channel that is involved in the detection and transduction of nociceptive stimuli. Inflammation and nerve damage result in the up-regulation of TRPV1 transcription, and, therefore, modulators of TRPV1 channels are potentially useful in the treatment of inflammatory and neuropathic pain. Understanding the binding modes of known ligands would significantly contribute to the success of TRPV1 modulator drug design programs. The recent cryo-electron microscopy structure of TRPV1 only provides a coarse characterization of the location of capsaicin (CAPS) and resiniferatoxin (RTX). Herein, we use the information contained in the experimental electron density maps to accurately determine the binding mode of CAPS and RTX and experimentally validate the computational results by mutagenesis. On the basis of these results, we perform a detailed analysis of TRPV1–ligand interactions, characterizing the protein ligand contacts and the role of individual water molecules. Importantly, our results provide a rational explanation and suggestion of TRPV1 ligand modifications that should improve binding affinity. PMID:26719417

  8. Emergence of multiple synchronization modes in hydrodynamically-coupled cilia

    NASA Astrophysics Data System (ADS)

    Guo, Hanliang; Kanso, Eva

    2016-11-01

    Motile cilia and flagella exhibit different phase coordinations. For example, closely swimming spermatozoa are observed to synchronize together; bi-flagellates Chlamydomonas regulate the flagella in a "breast-stroke" fashion; cilia on the surface of Paramecium beat in a fixed phase lag in an orchestrated wave like fashion. Experimental evidence suggests that phase coordinations can be achieved solely via hydrodynamical interactions. However, the exact mechanisms behind it remain illusive. Here, adapting a "geometric switch" model, we observe different synchronization modes in pairs of hydrodynamically-coupled cilia by changing physical parameters such as the strength of the cilia internal motor and the separation distance between cilia. Interestingly, we find regions in the parameter space where the coupled cilia reach stable phase coordinations and regions where the phase coordinations are sensitive to perturbations. We also find that leaning into the fluid reduces the sensitivity to perturbations, and produces stable phase coordination that is neither in-phase nor anti-phase, which could explain the origin of metachronal waves in large cilia populations.

  9. Rigorous Incorporation of Tautomers, Ionization Species, and Different Binding Modes into Ligand-Based and Receptor-Based 3D-QSAR Methods

    PubMed Central

    Natesan, Senthil; Balaz, Stefan

    2013-01-01

    Speciation of drug candidates and receptors caused by ionization, tautomerism, and/or covalent hydration complicates ligand- and receptor-based predictions of binding affinities by 3-dimensional structure-activity relationships (3D-QSAR). The speciation problem is exacerbated by tendency of tautomers to bind in multiple conformations or orientations (modes) in the same binding site. New forms of the 3D-QSAR correlation equations, capable of capturing this complexity, can be developed using the time hierarchy of all steps that lie behind the monitored biological process – binding, enzyme inhibition or receptor activity. In most cases, reversible interconversions of individual ligand and receptor species can be treated as quickly established equilibria because they are finished in a small fraction of the exposure time that is used to determine biological effects. The speciation equilibria are satisfactorily approximated by invariant fractions of individual ligand and receptor species for buffered experimental or in vivo conditions. For such situations, the observed drug-receptor association constant of a ligand is expressed as the sum of products, for each ligand and receptor species pair, of the association microconstant and the fractions of involved species. For multiple binding modes, each microconstant is expressed as the sum of microconstants of individual modes. This master equation leads to new 3D-QSAR correlation equations integrating the results of all molecular simulations or calculations, which are run for each ligand-receptor species pair separately. The multispecies, multimode 3D-QSAR approach is illustrated by a ligand-based correlation of transthyretin binding of thyroxine analogs and by a receptor-based correlation of inhibition of MK2 by benzothiophenes and pyrrolopyrimidines. PMID:23170882

  10. Global model of whistler mode chorus from multiple satellite observations

    NASA Astrophysics Data System (ADS)

    Meredith, Nigel; Horne, Richard; Sicard-Piet, Angelica; Boscher, Daniel; Yearby, Keith; Li, Wen; Thorne, Richard

    2013-04-01

    Gyroresonant wave particle interactions with whistler mode chorus play a fundamental role in the dynamics of the Earth's radiation belts and inner magnetosphere, affecting both the acceleration and loss of radiation belt electrons. Knowledge of the variability of chorus wave power as a function of both spatial location and geomagnetic activity, required for the computation of pitch angle and energy diffusion rates, is thus a critical input for global radiation belt models. Here we present a global model of lower band (0.1fce < f < 0.5fce) and upper band (0.5fce < f < fce) chorus, where fce is the local electron gyrofrequency, using plasma wave data from DE1, CRRES, Cluster 1, Double Star TC1 and THEMIS, extending the coverage and improving the statistics of existing models. The chorus emissions extend from the plasmapause out to L* = 10 and are found to be largely substorm dependent with the largest intensities being seen during active conditions. Equatorial lower band chorus is strongest during active conditions with peak intensities of the order 2000 pT2 in the region 4 < L* < 9 between 2300 and 1200 MLT. Equatorial upper band chorus is both weaker and less extensive with peak intensities of the order a few hundred pT2 during active conditions between 2300 and 1100 MLT from L* = 3 to L* = 7. Moving away from the equator mid-latitude chorus is strongest in the lower band during active conditions with peak intensities of the order 2000 pT2 in the region 4 < L* < 9 but is restricted to the dayside between 0700 and 1400 MLT. The results suggest that including wave particle interactions beyond geostationary orbit could be very important for global radiation belt models.

  11. Ocean Acidification Has Multiple Modes of Action on Bivalve Larvae

    PubMed Central

    Waldbusser, George G.; Hales, Burke; Langdon, Chris J.; Haley, Brian A.; Schrader, Paul; Brunner, Elizabeth L.; Gray, Matthew W.; Miller, Cale A.; Gimenez, Iria; Hutchinson, Greg

    2015-01-01

    Ocean acidification (OA) is altering the chemistry of the world’s oceans at rates unparalleled in the past roughly 1 million years. Understanding the impacts of this rapid change in baseline carbonate chemistry on marine organisms needs a precise, mechanistic understanding of physiological responses to carbonate chemistry. Recent experimental work has shown shell development and growth in some bivalve larvae, have direct sensitivities to calcium carbonate saturation state that is not modulated through organismal acid-base chemistry. To understand different modes of action of OA on bivalve larvae, we experimentally tested how pH, PCO2, and saturation state independently affect shell growth and development, respiration rate, and initiation of feeding in Mytilus californianus embryos and larvae. We found, as documented in other bivalve larvae, that shell development and growth were affected by aragonite saturation state, and not by pH or PCO2. Respiration rate was elevated under very low pH (~7.4) with no change between pH of ~ 8.3 to ~7.8. Initiation of feeding appeared to be most sensitive to PCO2, and possibly minor response to pH under elevated PCO2. Although different components of physiology responded to different carbonate system variables, the inability to normally develop a shell due to lower saturation state precludes pH or PCO2 effects later in the life history. However, saturation state effects during early shell development will carry-over to later stages, where pH or PCO2 effects can compound OA effects on bivalve larvae. Our findings suggest OA may be a multi-stressor unto itself. Shell development and growth of the native mussel, M. californianus, was indistinguishable from the Mediterranean mussel, Mytilus galloprovincialis, collected from the southern U.S. Pacific coast, an area not subjected to seasonal upwelling. The concordance in responses suggests a fundamental OA bottleneck during development of the first shell material affected only by

  12. Ocean Acidification Has Multiple Modes of Action on Bivalve Larvae.

    PubMed

    Waldbusser, George G; Hales, Burke; Langdon, Chris J; Haley, Brian A; Schrader, Paul; Brunner, Elizabeth L; Gray, Matthew W; Miller, Cale A; Gimenez, Iria; Hutchinson, Greg

    2015-01-01

    Ocean acidification (OA) is altering the chemistry of the world's oceans at rates unparalleled in the past roughly 1 million years. Understanding the impacts of this rapid change in baseline carbonate chemistry on marine organisms needs a precise, mechanistic understanding of physiological responses to carbonate chemistry. Recent experimental work has shown shell development and growth in some bivalve larvae, have direct sensitivities to calcium carbonate saturation state that is not modulated through organismal acid-base chemistry. To understand different modes of action of OA on bivalve larvae, we experimentally tested how pH, PCO2, and saturation state independently affect shell growth and development, respiration rate, and initiation of feeding in Mytilus californianus embryos and larvae. We found, as documented in other bivalve larvae, that shell development and growth were affected by aragonite saturation state, and not by pH or PCO2. Respiration rate was elevated under very low pH (~7.4) with no change between pH of ~ 8.3 to ~7.8. Initiation of feeding appeared to be most sensitive to PCO2, and possibly minor response to pH under elevated PCO2. Although different components of physiology responded to different carbonate system variables, the inability to normally develop a shell due to lower saturation state precludes pH or PCO2 effects later in the life history. However, saturation state effects during early shell development will carry-over to later stages, where pH or PCO2 effects can compound OA effects on bivalve larvae. Our findings suggest OA may be a multi-stressor unto itself. Shell development and growth of the native mussel, M. californianus, was indistinguishable from the Mediterranean mussel, Mytilus galloprovincialis, collected from the southern U.S. Pacific coast, an area not subjected to seasonal upwelling. The concordance in responses suggests a fundamental OA bottleneck during development of the first shell material affected only by

  13. Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.

    PubMed

    Khrapunovich-Baine, Marina; Menon, Vilas; Verdier-Pinard, Pascal; Smith, Amos B; Angeletti, Ruth Hogue; Fiser, Andras; Horwitz, Susan Band; Xiao, Hui

    2009-12-15

    The microtubule cytoskeleton has proven to be an effective target for cancer therapeutics. One class of drugs, known as microtubule stabilizing agents (MSAs), binds to microtubule polymers and stabilizes them against depolymerization. The prototype of this group of drugs, Taxol, is an effective chemotherapeutic agent used extensively in the treatment of human ovarian, breast, and lung carcinomas. Although electron crystallography and photoaffinity labeling experiments determined that the binding site for Taxol is in a hydrophobic pocket in beta-tubulin, little was known about the effects of this drug on the conformation of the entire microtubule. A recent study from our laboratory utilizing hydrogen-deuterium exchange (HDX) in concert with various mass spectrometry (MS) techniques has provided new information on the structure of microtubules upon Taxol binding. In the current study we apply this technique to determine the binding mode and the conformational effects on chicken erythrocyte tubulin (CET) of another MSA, discodermolide, whose synthetic analogues may have potential use in the clinic. We confirmed that, like Taxol, discodermolide binds to the taxane binding pocket in beta-tubulin. However, as opposed to Taxol, which has major interactions with the M-loop, discodermolide orients itself away from this loop and toward the N-terminal H1-S2 loop. Additionally, discodermolide stabilizes microtubules mainly via its effects on interdimer contacts, specifically on the alpha-tubulin side, and to a lesser extent on interprotofilament contacts between adjacent beta-tubulin subunits. Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo.

  14. Molecular Modeling Approaches to Study the Binding Mode on Tubulin of Microtubule Destabilizing and Stabilizing Agents

    NASA Astrophysics Data System (ADS)

    Botta, Maurizio; Forli, Stefano; Magnani, Matteo; Manetti, Fabrizio

    Tubulin targeting agents constitute an important class of anticancer drugs. By acting either as microtubule stabilizers or destabilizers, they disrupt microtubule dynamics, thus inducing mitotic arrest and, ultimately, cell death by apoptosis. Three different binding sites, whose exact location on tubulin has been experimentally detected, have been identified so far for antimitotic compound targeting microtubules, namely the taxoid, the colchicine and the vinka alkaloid binding site. A number of ligand- and structure-based molecular modeling studies in this field has been reported over the years, aimed at elucidating the binding modes of both stabilizing and destabilizing agent, as well as the molecular features responsible for their efficacious interaction with tubulin. Such studies are described in this review, focusing on information provided by different modeling approaches on the structural determinants of antitubulin agents and the interactions with the binding pockets on tubulin emerged as fundamental for antitumor activity.To describe molecular modeling approaches applied to date to molecules known to bind microtubules, this paper has been divided into two main parts: microtubule destabilizing (Part 1) and stabilizing (Part 2) agents. The first part includes structure-based and ligand-based approaches to study molecules targeting colchicine (1.1) and vinca alkaloid (1.2) binding sites, respectively. In the second part, the studies performed on microtubule-stabilizing antimitotic agents (MSAA) are described. Starting from the first representative compound of this class, paclitaxel, molecular modeling studies (quantitative structure-activity relationships - QSAR - and structure-based approaches), performed on natural compounds acting with the same mechanism of action and temptative common pharmacophoric hypotheses for all of these compounds, are reported.

  15. Exploring the DNA binding mode of transition metal based biologically active compounds

    NASA Astrophysics Data System (ADS)

    Raman, N.; Sobha, S.

    2012-01-01

    Few novel 4-aminoantipyrine derived Schiff bases and their metal complexes were synthesized and characterized. Their structural features and other properties were deduced from the elemental analysis, magnetic susceptibility and molar conductivity as well as from mass, IR, UV-vis, 1H NMR and EPR spectral studies. The binding of the complexes with CT-DNA was analyzed by electronic absorption spectroscopy, viscosity measurement, and cyclic voltammetry. The interaction of the metal complexes with DNA was also studied by molecular modeling with special reference to docking. The experimental and docking results revealed that the complexes have the ability of interaction with DNA of minor groove binding mode. The intrinsic binding constants ( Kb) of the complexes with CT-DNA were found out which show that they are minor groove binders. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pUC19 DNA in the presence of AH 2 (ascorbic acid). Moreover, the oxidative cleavage studies using distamycin revealed the minor groove binding for the newly synthesized 4-aminoantipyrine derived Schiff bases and their metal complexes. Evaluation of antibacterial activity of the complexes against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and Klebsiella pneumoniae exhibited that the complexes have potent biocidal activity than the free ligands.

  16. Mapping inhibitor binding modes on an active cysteine protease via nuclear magnetic resonance spectroscopy.

    PubMed

    Lee, Gregory M; Balouch, Eaman; Goetz, David H; Lazic, Ana; McKerrow, James H; Craik, Charles S

    2012-12-18

    Cruzain is a member of the papain/cathepsin L family of cysteine proteases, and the major cysteine protease of the protozoan Trypanosoma cruzi, the causative agent of Chagas disease. We report an autoinduction methodology that provides soluble cruzain in high yields (>30 mg/L in minimal medium). These increased yields provide sufficient quantities of active enzyme for use in nuclear magnetic resonance (NMR)-based ligand mapping. Using circular dichroism and NMR spectroscopy, we also examined the solution-state structural dynamics of the enzyme in complex with a covalently bound vinyl sulfone inhibitor (K777). We report the backbone amide and side chain carbon chemical shift assignments of cruzain in complex with K777. These resonance assignments were used to identify and map residues located in the substrate binding pocket, including the catalytic Cys25 and His162. Selective [(15)N]Cys, [(15)N]His, and [(13)C]Met labeling was performed to quickly assess cruzain-ligand interactions for a set of eight low-molecular weight compounds exhibiting micromolar binding or inhibition. Chemical shift perturbation mapping verified that six of the eight compounds bind to cruzain at the active site. Three different binding modes were delineated for the compounds, namely, covalent, noncovalent, and noninteracting. These results provide examples of how NMR spectroscopy can be used to screen compounds for fast evaluation of enzyme-inhibitor interactions to facilitate lead compound identification and subsequent structural studies.

  17. Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA.

    PubMed

    Xia, Kaixin; Zhang, Guowen; Gong, Deming

    2017-01-24

    The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive.

  18. Exploring the DNA binding mode of transition metal based biologically active compounds.

    PubMed

    Raman, N; Sobha, S

    2012-01-01

    Few novel 4-aminoantipyrine derived Schiff bases and their metal complexes were synthesized and characterized. Their structural features and other properties were deduced from the elemental analysis, magnetic susceptibility and molar conductivity as well as from mass, IR, UV-vis, (1)H NMR and EPR spectral studies. The binding of the complexes with CT-DNA was analyzed by electronic absorption spectroscopy, viscosity measurement, and cyclic voltammetry. The interaction of the metal complexes with DNA was also studied by molecular modeling with special reference to docking. The experimental and docking results revealed that the complexes have the ability of interaction with DNA of minor groove binding mode. The intrinsic binding constants (K(b)) of the complexes with CT-DNA were found out which show that they are minor groove binders. Gel electrophoresis assay demonstrated the ability of the complexes to cleave the pUC19 DNA in the presence of AH(2) (ascorbic acid). Moreover, the oxidative cleavage studies using distamycin revealed the minor groove binding for the newly synthesized 4-aminoantipyrine derived Schiff bases and their metal complexes. Evaluation of antibacterial activity of the complexes against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, and Klebsiella pneumoniae exhibited that the complexes have potent biocidal activity than the free ligands.

  19. Distinct ETA Receptor Binding Mode of Macitentan As Determined by Site Directed Mutagenesis

    PubMed Central

    Gatfield, John; Mueller Grandjean, Celia; Bur, Daniel; Bolli, Martin H.; Nayler, Oliver

    2014-01-01

    The competitive endothelin receptor antagonists (ERA) bosentan and ambrisentan, which have long been approved for the treatment of pulmonary arterial hypertension, are characterized by very short (1 min) occupancy half-lives at the ETA receptor. The novel ERA macitentan, displays a 20-fold increased receptor occupancy half-life, causing insurmountable antagonism of ET-1-induced signaling in pulmonary arterial smooth muscle cells. We show here that the slow ETA receptor dissociation rate of macitentan was shared with a set of structural analogs, whereas compounds structurally related to bosentan displayed fast dissociation kinetics. NMR analysis showed that macitentan adopts a compact structure in aqueous solution and molecular modeling suggests that this conformation tightly fits into a well-defined ETA receptor binding pocket. In contrast the structurally different and negatively charged bosentan-type molecules only partially filled this pocket and expanded into an extended endothelin binding site. To further investigate these different ETA receptor-antagonist interaction modes, we performed functional studies using ETA receptor variants harboring amino acid point mutations in the presumed ERA interaction site. Three ETA receptor residues significantly and differentially affected ERA activity: Mutation R326Q did not affect the antagonist activity of macitentan, however the potencies of bosentan and ambrisentan were significantly reduced; mutation L322A rendered macitentan less potent, whereas bosentan and ambrisentan were unaffected; mutation I355A significantly reduced bosentan potency, but not ambrisentan and macitentan potencies. This suggests that – in contrast to bosentan and ambrisentan - macitentan-ETA receptor binding is not dependent on strong charge-charge interactions, but depends predominantly on hydrophobic interactions. This different binding mode could be the reason for macitentan's sustained target occupancy and insurmountable antagonism. PMID

  20. Dynamics in the DNA recognition by DAPI: exploration of the various binding modes.

    PubMed

    Banerjee, Debapriya; Pal, Samir Kumar

    2008-01-24

    Two distinct modes of interaction of the fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), depending on the sequence of DNA, have been reported in the literature. In the present study, the dynamics of solvation has been utilized to explore the binding interaction of DAPI to DNA oligomers of different sequences. Picosecond-resolved fluorescence and polarization-gated anisotropy have been used to characterize the binding of DAPI to the different oligomers. In the double-stranded dodecamer of sequence CGCGAATTCGCG (oligo1), the solvation relaxation dynamics of the probe reveals time constants of 0.130 ns (75%) and 2.35 ns (25%). Independent exploration of the minor-groove environment of oligo1 using another well-known minor-groove binder Hoechst 33258 (H258) shows similar timescales, further confirming minor-groove binding of DAPI to oligo1. In the double-stranded dodecamer (oligo2) having the sequence GCGCGCGCGCGC, where intercalation has been reported in the literature, no solvation is observed in our experimental window. DAPI bound to oligo2 shows quenching of fluorescence compared to that of DAPI in a buffer. The quenching of fluorescence of DAPI intercalated in DNA is also borne out by the appearance of a fast component of 30 ps in the fluorescence lifetime, revealing electron transfer to DAPI from GC base pairs, between which it intercalates. In addition to this, the excited-state lifetime of the probe in the DAPI-DNA complex also shows a time constant similar to that of the dye in a buffer, indicating that the excited-state photoprocesses associated with the free dye is also operative in this binding mode, consistent with the binding geometry of the DAPI in the DNA. The dynamics of DAPI in calf thymus DNA having a random sequence of base pairs is similar to that associated with the DNA minor groove. Our studies clearly explore the structure-dynamics correlation of the DAPI-DNA complex in the two distinct modes of interaction of DAPI with DNA.

  1. Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations.

    PubMed

    Tripathi, Shubhandra; Kumar, Akhil; Kumar, B Sathish; Negi, Arvind S; Sharma, Ashok

    2016-06-01

    Microtubule stabilizers provide an important mode of treatment via mitotic cell arrest of cancer cells. Recently, we reported two novel neolignans derivatives Cmp10 and Cmp19 showing anticancer activity and working as microtubule stabilizers at micromolar concentrations. In this study, we have explored the binding site, mode of binding, and stabilization by two novel microtubule stabilizers Cmp10 and Cmp19 using in silico molecular docking, molecular dynamics (MD) simulation, and binding free energy calculations. Molecular docking studies were performed to explore the β-tubulin binding site of Cmp10 and Cmp19. Further, MD simulations were used to probe the β-tubulin stabilization mechanism by Cmp10 and Cmp19. Binding affinity was also compared for Cmp10 and Cmp19 using binding free energy calculations. Our docking results revealed that both the compounds bind at Ptxl binding site in β-tubulin. MD simulation studies showed that Cmp10 and Cmp19 binding stabilizes M-loop (Phe272-Val288) residues of β-tubulin and prevent its dynamics, leading to a better packing between α and β subunits from adjacent tubulin dimers. In addition, His229, Ser280 and Gln281, and Arg278, Thr276, and Ser232 were found to be the key amino acid residues forming H-bonds with Cmp10 and Cmp19, respectively. Consequently, binding free energy calculations indicated that Cmp10 (-113.655 kJ/mol) had better binding compared to Cmp19 (-95.216 kJ/mol). This study provides useful insight for better understanding of the binding mechanism of Cmp10 and Cmp19 and will be helpful in designing novel microtubule stabilizers.

  2. High-speed multiple-mode mass-sensing resolves dynamic nanoscale mass distributions

    PubMed Central

    Olcum, Selim; Cermak, Nathan; Wasserman, Steven C.; Manalis, Scott R.

    2015-01-01

    Simultaneously measuring multiple eigenmode frequencies of nanomechanical resonators can determine the position and mass of surface-adsorbed proteins, and could ultimately reveal the mass tomography of nanoscale analytes. However, existing measurement techniques are slow (<1 Hz bandwidth), limiting throughput and preventing use with resonators generating fast transient signals. Here we develop a general platform for independently and simultaneously oscillating multiple modes of mechanical resonators, enabling frequency measurements that can precisely track fast transient signals within a user-defined bandwidth that exceeds 500 Hz. We use this enhanced bandwidth to resolve signals from multiple nanoparticles flowing simultaneously through a suspended nanochannel resonator and show that four resonant modes are sufficient for determining their individual position and mass with an accuracy near 150 nm and 40 attograms throughout their 150-ms transit. We envision that our method can be readily extended to other systems to increase bandwidth, number of modes, or number of resonators. PMID:25963304

  3. Development of optimal design theory for series multiple tuned mass dampers considering stroke and multiple structural modes

    NASA Astrophysics Data System (ADS)

    Wang, J. F.; Lin, C. C.

    2016-09-01

    A tuned mass damper (TMD) system generates structural control forces through large motions of mass units. Therefore, it may not be functional if the stroke capacity of its spring and damper components are insufficient. This paper focuses on a novel mass-damper system, the series multiple tuned mass damper (SMTMD) system, which consists of multiple interconnected TMDs, of which only the first is connected to the primary structure. The main purpose of this paper is to compare the control effectiveness and TMD stroke of SMTMDs with those of a conventional TMD device. In addition, the ability of the studied SMTMD to suppress multiple structural modes is also investigated. First, the optimal design theory for an SMTMD installed on an arbitrary floor of a multi-storey building is developed. To optimize the SMTMD parameters, two performance indices are established by combining multiple modal responses of the primary structure. The developed theory is demonstrated analytically by using a three-story building. The results show that the SMTMD with a higher number of TMD units places lower demands on the TMD stroke and is more adaptive in controlling multiple structural modes of the primary structure.

  4. Studies of the binding mode of TXNHCH2COOH with calf thymus DNA by spectroscopic methods

    NASA Astrophysics Data System (ADS)

    Ataci, Nese; Arsu, Nergis

    2016-12-01

    In this study, a thioxanthone derivative named 2-(9-oxo-9H-thioxanthen-2ylamino) acetic acid (TX-NHCH2COOH) was used to investigate small molecule and DNA binding interactions. Absorption and fluorescence emission spectroscopy were used and melting studies were used to explain the binding mode of TXNHCH2COOH-DNA. Intrinsic binding constant Kb TXNHCH2COOH was found 6 × 105 M- 1from UV-Vis absorption spectroscopy. Fluorescence emmision intensity increased by adding ct-DNA to the TXNHCH2COOH and KI quenching experiments resulted with low Ksv value. Additionally, 3.7 °C increase for Tm was observed. The observed quenching of EB and ct-DNA complex and increase viscosity values of ct-DNA by addition of TXNHCH2COOH was determined. All those results indicate that TXNHCH2COOH can intercalate into DNA base pairs. Fluorescence microscopy helped to display imaging of the TXNHCH2COOH-DNA solution.

  5. Dynamic Binding Mode of a Synaptotagmin-1-SNARE Complex in Solution

    PubMed Central

    Brewer, Kyle D.; Bacaj, Taulant; Cavalli, Andrea; Camilloni, Carlo; Swarbrick, James D.; Liu, Jin; Zhou, Amy; Zhou, Peng; Barlow, Nicholas; Xu, Junjie; Seven, Alpay B.; Prinslow, Eric A.; Voleti, Rashmi; Häussinger, Daniel; Bonvin, Alexandre M.J.J.; Tomchick, Diana R.; Vendruscolo, Michele; Graham, Bim; Südhof, Thomas C.; Rizo, Josep

    2015-01-01

    SUMMARY Rapid neurotransmitter release depends on the Ca2+-sensor Synaptotagmin-1 and the SNARE complex formed by synaptobrevin, syntaxin-1 and SNAP-25. How Synaptotagmin-1 triggers release remains unclear, in part because elucidating high-resolution structures of Synaptotagmin-1-SNARE complexes has been challenging. An NMR approach based on lanthanide-induced pseudocontact shifts now reveals a dynamic binding mode where basic residues in the concave side of the Synaptotagmin-1 C2B domain β-sandwich interact with a polyacidic region of the SNARE complex formed by syntaxin-1 and SNAP-25. The physiological relevance of this dynamic structural model is supported by mutations in basic residues of Synaptotagmin-1 that markedly impair SNARE-complex binding in vitro and Synaptotagmin-1 function in neurons. Mutations with milder effects on binding have correspondingly milder effects on Synaptotagmin-1 function. Our results support a model whereby their dynamic interaction facilitates cooperation between synaptotagmin-1 and the SNAREs in inducing membrane fusion. PMID:26030874

  6. Tau proteins: the molecular structure and mode of binding on microtubules

    PubMed Central

    1988-01-01

    Tau is a family of closely related proteins (55,000-62,000 mol wt) which are contained in the nerve cells and copolymerize with tubulin to induce the formation of microtubules in vitro. All information so far has indicated that tau is closely apposed to the microtubule lattice, and there was no indication of domains projecting from the microtubule polymer lattice. We have studied the molecular structure of the tau factor and its mode of binding on microtubules using the quick-freeze, deep-etch method (QF.DE) and low angle rotary shadowing technique. Phosphocellulose column-purified tubulin from porcine brain was polymerized with tau and the centrifuged pellets were processed by QF.DE. We observed periodic armlike elements (18.7 +/- 4.8 nm long) projecting from the microtubule surface. Most of the projections appeared to cross-link adjacent microtubules. We measured the longitudinal periodicity of tau projections on the microtubules and found it to match the 6-dimer pattern better than the 12-dimer pattern. The stoichiometry of tau versus tubulin in preparations of tau saturated microtubules was 1:approximately 5.0 (molar ratio). Tau molecules adsorbed on mica took on rodlike forms (56.1 +/- 14.1 nm long). Although both tau and MAP1 are contained in axons, competitive binding studies demonstrated that the binding sites of tau and MAP1A on the microtubule surfaces are most distinct, although they may partially overlap. PMID:3139677

  7. Normal Modes for Dynamic Motions of a Topoisomerase II enzyme upon DNA-Binding and Bending

    NASA Astrophysics Data System (ADS)

    Mentes, Ahmet

    We have used Molecular Dynamics (MD) simulation methods and two analytical approaches (the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM)) to investigate the internal dynamic motions of the S. cerevisiae Topoisomerase (TopoII) during the first step of its catalytic cycle. At the initial state of the first step of its catalytic cycle, the protein and a 34 bp straight-DNA structure have no interaction. At the final state of the cycle, we have the bended-DNA/TopoII complex where the protein binds to DNA and, at this stage, the protein binds and bends the DNA, just before the DNA cleavage by TopoII. Normal mode analysis is used to characterize the functional flexibility of the protein, especially the C-gate domain closing/opening during the DNA binding/bending process and before DNA cleavage. Because of its clinical importance, our study might be helpful to better understand the next steps of its catalytic cycle and may provide new insight into the dynamics and structure of other TopoII-DNA complexes.

  8. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

    DOE PAGES

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; ...

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes withmore » different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.« less

  9. DNA binding mode of novel tetradentate amino acid based 2-hydroxybenzylidene-4-aminoantipyrine complexes

    NASA Astrophysics Data System (ADS)

    Raman, N.; Sobha, S.; Selvaganapathy, M.; Mahalakshmi, R.

    2012-10-01

    Few transition metal complexes of tetradentate N2O2 donor Schiff base ligands containing 2-hydroxybenzylidene-4-aminoantipyrine and amino acids (alanine/valine) abbreviated to KHL1/KHL2 have been synthesized. All the metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The Schiff bases KHL1/KHL2 are found to act as tetradentate ligands using N2O2 donor set of atoms leading to a square-planar geometry for the complexes around the metal ions. The binding behaviors of the complexes to calf thymus DNA have been investigated by absorption spectra, viscosity measurements and cyclic voltammetry. The DNA binding constants reveal that all these complexes interact with DNA through minor groove binding mode. The studies on mechanism of photocleavage reveal that singlet oxygen (1O2) and superoxide anion radical (O2rad -) may play an important role in the photocleavage. The Schiff bases and their metal complexes have been screened for their in vitro antibacterial activities against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae and antifungal activities against Aspergillus niger, Fusarium solani, Culvularia lunata, Rhizoctonia bataicola and Candida albicans by MIC method.

  10. A Novel Cofactor-binding Mode in Bacterial IMP Dehydrogenases Explains Inhibitor Selectivity*

    PubMed Central

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; Joachimiak, Andrzej

    2015-01-01

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5′-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization. PMID:25572472

  11. Phthalocyanine tetrasulfonates bind to multiple sites on natively-folded prion protein.

    PubMed

    Dee, Derek R; Gupta, Amar Nath; Anikovskiy, Max; Sosova, Iveta; Grandi, Elena; Rivera, Laura; Vincent, Abhilash; Brigley, Angela M; Petersen, Nils O; Woodside, Michael T

    2012-06-01

    The phthalocyanine tetrasulfonates (PcTS), a class of cyclic tetrapyrroles, bind to the mammalian prion protein, PrP. Remarkably, they can act as anti-scrapie agents to prevent the formation and spread of infectious, misfolded PrP. While the effects of phthalocyanines on the diseased state have been investigated, the interaction between PcTS and PrP has not yet been extensively characterized. Here we use multiple, complementary assays (surface plasmon resonance, isothermal titration calorimetry, fluorescence correlation spectroscopy, and tryptophan fluorescence quenching) to characterize the binding of PcTS to natively-folded hamster PrP(90-232), in order to determine binding constants, ligand stoichiometry, influence of buffer ionic strength, and the effects of chelated metal ions. We found that binding strength depends strongly on chelated metal ions, with Al(3+)-PcTS binding the weakest and free-base PcTS the strongest of the three types tested (Al(3+), Zn(2+), and free-base). Buffer ionic strength also affected the binding, with K(d) increasing along with salt concentration. The binding isotherms indicated the presence of at least two different binding sites with micromolar affinities and a total stoichiometry of ~4-5 PcTS molecules per PrP molecule.

  12. Multiple-soliton dynamic patterns in a graphene mode-locked fiber laser.

    PubMed

    Meng, Yichang; Zhang, Shumin; Li, Xingliang; Li, Hongfei; Du, Juan; Hao, Yanping

    2012-03-12

    Multiple-soliton dynamic patterns have been observed experimentally in an erbium-doped fiber ring laser with graphene as a saturable absorber. Under relatively low pumping power we have obtained disordered multiple-solitons, bunched solitons and high order harmonic mode locking by adjusting the orientation of the polarization controllers. With increased pumping power, we have also observed flow of solitons. We have experimentally investigated in detail the conditions under which these patterns form.

  13. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, Sanghamitra; Ghosh, Dip; Mitra, Ramkrishna; Zhao, Zhongming

    2015-01-01

    MicroRNA (miRNA) regulates gene expression by binding to specific sites in the 3'untranslated regions of its target genes. Machine learning based miRNA target prediction algorithms first extract a set of features from potential binding sites (PBSs) in the mRNA and then train a classifier to distinguish targets from non-targets. However, they do not consider whether the PBSs are functional or not, and consequently result in high false positive rates. This substantially affects the follow up functional validation by experiments. We present a novel machine learning based approach, MBSTAR (Multiple instance learning of Binding Sites of miRNA TARgets), for accurate prediction of true or functional miRNA binding sites. Multiple instance learning framework is adopted to handle the lack of information about the actual binding sites in the target mRNAs. Biologically validated 9531 interacting and 973 non-interacting miRNA-mRNA pairs are identified from Tarbase 6.0 and confirmed with PAR-CLIP dataset. It is found that MBSTAR achieves the highest number of binding sites overlapping with PAR-CLIP with maximum F-Score of 0.337. Compared to the other methods, MBSTAR also predicts target mRNAs with highest accuracy. The tool and genome wide predictions are available at http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm.

  14. Zinc-induced oligomerization of zinc α2 glycoprotein reveals multiple fatty acid-binding sites.

    PubMed

    Zahid, Henna; Miah, Layeque; Lau, Andy M; Brochard, Lea; Hati, Debolina; Bui, Tam T T; Drake, Alex F; Gor, Jayesh; Perkins, Stephen J; McDermott, Lindsay C

    2016-01-01

    Zinc α2 glycoprotein (ZAG) is an adipokine with a class I MHC protein fold and is associated with obesity and diabetes. Although its intrinsic ligand remains unknown, ZAG binds the dansylated C11 fatty acid 11-(dansylamino)undecanoic acid (DAUDA) in the groove between the α1 and α2 domains. The surface of ZAG has approximately 15 weak zinc-binding sites deemed responsible for precipitation from human plasma. In the present study the functional significance of these metal sites was investigated. Analytical ultracentrifugation (AUC) and CD showed that zinc, but not other divalent metals, causes ZAG to oligomerize in solution. Thus ZAG dimers and trimers were observed in the presence of 1 and 2 mM zinc. Molecular modelling of X-ray scattering curves and sedimentation coefficients indicated a progressive stacking of ZAG monomers, suggesting that the ZAG groove may be occluded in these. Using fluorescence-detected sedimentation velocity, these ZAG-zinc oligomers were again observed in the presence of the fluorescent boron dipyrromethene fatty acid C16-BODIPY (4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-hexadecanoic acid). Fluorescence spectroscopy confirmed that ZAG binds C16-BODIPY. ZAG binding to C16-BODIPY, but not to DAUDA, was reduced by increased zinc concentrations. We conclude that the lipid-binding groove in ZAG contains at least two distinct fatty acid-binding sites for DAUDA and C16-BODIPY, similar to the multiple lipid binding seen in the structurally related immune protein CD1c. In addition, because high concentrations of zinc occur in the pancreas, the perturbation of these multiple lipid-binding sites by zinc may be significant in Type 2 diabetes where dysregulation of ZAG and zinc homoeostasis occurs.

  15. Benzimidazole inhibitors of the protein kinase CHK2: clarification of the binding mode by flexible side chain docking and protein-ligand crystallography.

    PubMed

    Matijssen, Cornelis; Silva-Santisteban, M Cris; Westwood, Isaac M; Siddique, Samerene; Choi, Vanessa; Sheldrake, Peter; van Montfort, Rob L M; Blagg, Julian

    2012-11-15

    Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature.

  16. Benzimidazole inhibitors of the protein kinase CHK2: Clarification of the binding mode by flexible side chain docking and protein–ligand crystallography

    PubMed Central

    Matijssen, Cornelis; Silva-Santisteban, M. Cris; Westwood, Isaac M.; Siddique, Samerene; Choi, Vanessa; Sheldrake, Peter; van Montfort, Rob L.M.; Blagg, Julian

    2012-01-01

    Two closely related binding modes have previously been proposed for the ATP-competitive benzimidazole class of checkpoint kinase 2 (CHK2) inhibitors; however, neither binding mode is entirely consistent with the reported SAR. Unconstrained rigid docking of benzimidazole ligands into representative CHK2 protein crystal structures reveals an alternative binding mode involving a water-mediated interaction with the hinge region; docking which incorporates protein side chain flexibility for selected residues in the ATP binding site resulted in a refinement of the water-mediated hinge binding mode that is consistent with observed SAR. The flexible docking results are in good agreement with the crystal structures of four exemplar benzimidazole ligands bound to CHK2 which unambiguously confirmed the binding mode of these inhibitors, including the water-mediated interaction with the hinge region, and which is significantly different from binding modes previously postulated in the literature. PMID:23058106

  17. Multiple opioid receptor binding in dissociated intact guinea pig brain cells

    SciTech Connect

    Tam, S.W.; James, D.W.

    1986-03-05

    Dissociated intact guinea pig brain cells were prepared by the method of Rogers and El-Fakahany. Over 95% of these cells are viable as demonstrated by their exclusion of the dye trypan blue. Opioid receptor binding assays were performed in a modified Kreb-Ringers physiological buffer. The following radiolabeled ligands and conditions were used to selectively labeled multiple opioid receptors: mu binding, 1 nM (/sup 3/H)naloxone + 20 nM DADLE + 300 nM U50,488H; kappa binding, 4 nM (-)-(/sup 3/H)-EKC + 100 nM DAGO + 500 nM DADLE; delta binding, 2 nM (/sup 3/H)-DADLE + 100 nM DAGO + 300 nM U50,488H; sigma binding, 4 nM (+)-(/sup 3/H)SKF 10,047. The intact brain cells in physiological buffer demonstrated specific binding for mu, kappa, delta, and sigma receptors. The relative binding potency of naloxone for each of the receptor types is arbitrarily set at 1.

  18. Binding Mode of Acetylated Histones to Bromodomains: Variations on a Common Motif.

    PubMed

    Marchand, Jean-Rémy; Caflisch, Amedeo

    2015-08-01

    Bromodomains, epigenetic readers that recognize acetylated lysine residues in histone tails, are potential drug targets in cancer and inflammation. Herein we review the crystal structures of human bromodomains in complex with histone tails and analyze the main interaction motifs. The histone backbone is extended and occupies, in one of the two possible orientations, the bromodomain surface groove lined by the ZA and BC loops. The acetyl-lysine side chain is buried in the cavity between the four helices of the bromodomain, and its oxygen atom accepts hydrogen bonds from a structural water molecule and a conserved asparagine residue in the BC loop. In stark contrast to this common binding motif, a large variety of ancillary interactions emerge from our analysis. In 10 of 26 structures, a basic side chain (up to five residues up- or downstream in sequence with respect to the acetyl-lysine) interacts with the carbonyl groups of the C-terminal turn of helix αB. Furthermore, the complexes reveal many heterogeneous backbone hydrogen bonds (direct or water-bridged). These interactions contribute unselectively to the binding of acetylated histone tails to bromodomains, which provides further evidence that specific recognition is modulated by combinations of multiple histone modifications and multiple modules of the proteins involved in transcription.

  19. A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer

    PubMed Central

    Forés, Marta; Samper, Núria; Barbacid, Mariano

    2017-01-01

    HMG-box proteins, including Sox/SRY (Sox) and TCF/LEF1 (TCF) family members, bind DNA via their HMG-box. This binding, however, is relatively weak and both Sox and TCF factors employ distinct mechanisms for enhancing their affinity and specificity for DNA. Here we report that Capicua (CIC), an HMG-box transcriptional repressor involved in Ras/MAPK signaling and cancer progression, employs an additional distinct mode of DNA binding that enables selective recognition of its targets. We find that, contrary to previous assumptions, the HMG-box of CIC does not bind DNA alone but instead requires a distant motif (referred to as C1) present at the C-terminus of all CIC proteins. The HMG-box and C1 domains are both necessary for binding specific TGAATGAA-like sites, do not function via dimerization, and are active in the absence of cofactors, suggesting that they form a bipartite structure for sequence-specific binding to DNA. We demonstrate that this binding mechanism operates throughout Drosophila development and in human cells, ensuring specific regulation of multiple CIC targets. It thus appears that HMG-box proteins generally depend on auxiliary DNA binding mechanisms for regulating their appropriate genomic targets, but that each sub-family has evolved unique strategies for this purpose. Finally, the key role of C1 in DNA binding also explains the fact that this domain is a hotspot for inactivating mutations in oligodendroglioma and other tumors, while being preserved in oncogenic CIC-DUX4 fusion chimeras associated to Ewing-like sarcomas. PMID:28278156

  20. A Novel Approach to Beam Steering Using Arrays Composed of Multiple Unique Radiating Modes

    NASA Astrophysics Data System (ADS)

    Labadie, Nathan Richard

    Phased array antennas have found wide application in both radar and wireless communications systems particularly as implementation costs continue to decrease. The primary advantages of electronically scanned arrays are speed of beam scan and versatility of beamforming compared to mechanically scanned fixed beam antennas. These benefits come at the cost of a few well known design issues including element pattern rolloff and mutual coupling between elements. Our primary contribution to the field of research is the demonstration of significant improvement in phased array scan performance using multiple unique radiating modes. In short, orthogonal radiating modes have minimal coupling by definition and can also be generated with reduced rolloff at wide scan angles. In this dissertation, we present a combination of analysis, full-wave electromagnetic simulation and measured data to support our claims. The novel folded ring resonator (FRR) antenna is introduced as a wideband and multi-band element embedded in a grounded dielectric substrate. Multiple radiating modes of a small ground plane excited by a four element FRR array were also investigated. A novel hemispherical null steering antenna composed of two collocated radiating elements, each supporting a unique radiating mode, is presented in the context of an anti-jam GPS receiver application. Both the antenna aperture and active feed network were fabricated and measured showing excellent agreement with analytical and simulated data. The concept of using an antenna supporting multiple radiating modes for beam steering is also explored. A 16 element hybrid linear phased array was fabricated and measured demonstrating significantly improved scan range and scanned gain compared to a conventional phased array. This idea is expanded to 2 dimensional scanning arrays by analysis and simulation of a hybrid phased array composed of novel multiple mode monopole on patch antenna sub-arrays. Finally, we fabricated and

  1. The Mode of Hedgehog Binding to Ihog Homologues is Not Conserved Across Different Phyla

    SciTech Connect

    McLellan, J.; Zheng, X; Hauk, G; Ghirlando, R; Beachy, P; Leahy, D

    2008-01-01

    Hedgehog (Hh) proteins specify tissue pattern in metazoan embryos by forming gradients that emanate from discrete sites of expression and elicit concentration-dependent cellular differentiation or proliferation responses1, 2. Cellular responses to Hh and the movement of Hh through tissues are both precisely regulated, and abnormal Hh signalling has been implicated in human birth defects and cancer3, 4, 5, 6, 7. Hh signalling is mediated by its amino-terminal domain (HhN), which is dually lipidated and secreted as part of a multivalent lipoprotein particle8, 9, 10. Reception of the HhN signal is modulated by several cell-surface proteins on responding cells, including Patched (Ptc), Smoothened (Smo), Ihog (known as CDO or CDON in mammals) and the vertebrate-specific proteins Hip (also known as Hhip) and Gas1 (ref. 11). Drosophila Ihog and its vertebrate homologues CDO and BOC contain multiple immunoglobulin and fibronectin type III (FNIII) repeats, and the first FNIII repeat of Ihog binds Drosophila HhN in a heparin-dependent manner12, 13. Surprisingly, pull-down experiments suggest that a mammalian Sonic hedgehog N-terminal domain (ShhN) binds a non-orthologous FNIII repeat of CDO12, 14. Here we report biochemical, biophysical and X-ray structural studies of a complex between ShhN and the third FNIII repeat of CDO. We show that the ShhN-CDO interaction is completely unlike the HhN-Ihog interaction and requires calcium, which binds at a previously undetected site on ShhN. This site is conserved in nearly all Hh proteins and is a hotspot for mediating interactions between ShhN and CDO, Ptc, Hip and Gas1. Mutations in vertebrate Hh proteins causing holoprosencephaly and brachydactyly type A1 map to this calcium-binding site and disrupt interactions with these partners.

  2. Mode of bindings of zinc oxide nanoparticles to myoglobin and horseradish peroxidase: A spectroscopic investigations

    NASA Astrophysics Data System (ADS)

    Mandal, Gopa; Bhattacharya, Sudeshna; Ganguly, Tapan

    2011-07-01

    The interactions between two heme proteins myoglobin (HMb) and horseradish peroxidase (HRP) with zinc oxide (ZnO) nanoparticles are investigated by using UV-vis absorption, steady state fluorescence, synchronous fluorescence, time-resolved fluorescence, FT-IR, atomic force microscopy (AFM) and circular dichroism (CD) techniques under physiological condition of pH˜7.4. The presence of mainly static mode in fluorescence quenching mechanism of HMb and HRP by ZnO nanoparticle indicates the possibility of formation of ground state complex. The processes of bindings of ZnO nanoparticles with the two proteins are spontaneous molecular interaction procedures. In both cases hydrogen bonding plays a major role. The circular dichroism (CD) spectra reveal that a helicity of the proteins is reduced by increasing ZnO nanoparticle concentration although the α-helical structures of HMb and HRP retain their identity. On binding to the ZnO nanoparticles the secondary structure of HRP molecules (or HMb molecules) remains unchanged while there is a substantial change in the environment of the tyrosin active site in case of HRP molecules and tryptophan active site in case of HMb molecules. Tapping mode atomic force microscopy (AFM) was applied for the investigation the structure of HRP adsorbed in the environment of nanoparticles on the silicon and on the bare silicon. HRP molecules adsorb and aggregate on the mica with ZnO nanoparticle. The aggregation indicates an attractive interaction among the adsorbed molecules. The molecules are randomly distributed on the bare silicon wafer. The adsorption of HRP in the environment of ZnO nanoparticle changes drastically the domains due to a strong interaction between HRP and ZnO nanoparticles. Similar situation is observed in case of HMb molecules. These findings demonstrate the efficacy of biomedical applications of ZnO nanoparticles as well as in elucidating their mechanisms of action as drugs in both human and plant systems.

  3. Pharmacophore modeling, comprehensive 3D-QSAR, and binding mode analysis of TGR5 agonists.

    PubMed

    Sindhu, Thangaraj; Srinivasan, Pappu

    2017-04-01

    Takeda G-protein-coupled receptor 5 (TGR5) is emerging as an important and promising target for the development of anti-diabetic drugs. Pharmacophore modeling and atom-based 3D-QSAR studies were carried out on a new series of 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides as highly potent agonists of TGR5. The generated best six featured pharmacophore model AAHHRR consists of two hydrogen bond acceptors (A): two hydrophobic groups (H) and two aromatic rings (R). The constructed 3D-QSAR model acquired excellent correlation coefficient value (R(2 )=( )0.9018), exhibited good predictive power (Q(2 )=( )0.8494) and high Fisher ratio (F = 61.2). The pharmacophore model was validated through Guner-Henry (GH) scoring method. The GH value of 0.5743 indicated that the AAHHRR model was statistically valuable and reliable in the identification of TGR5 agonists. Furthermore, the combined approach of molecular docking and binding free energy calculations were carried out for the 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides to explore the binding mode and interaction pattern. The generated contour maps revealed the important structural insights for the activity of the compounds. The results obtained from this study could be helpful in the development of novel and more potent agonists of TGR5.

  4. Substrate binding mode and reaction mechanism of undecaprenyl pyrophosphate synthase deduced from crystallographic studies.

    PubMed

    Chang, Sing-Yang; Ko, Tzu-Ping; Chen, Annie P-C; Wang, Andrew H-J; Liang, Po-Huang

    2004-04-01

    Undecaprenyl pyrophosphate synthase (UPPs) catalyzes eight consecutive condensation reactions of farnesyl pyrophosphate (FPP) with isopentenyl pyrophosphate (IPP) to form a 55-carbon long-chain product. We previously reported the crystal structure of the apo-enzyme from Escherichia coli and the structure of UPPs in complex with sulfate ions (resembling pyrophosphate of substrate), Mg(2+), and two Triton molecules (product-like). In the present study, FPP substrate was soaked into the UPPs crystals, and the complex structure was solved. Based on the crystal structure, the pyrophosphate head group of FPP is bound to the backbone NHs of Gly29 and Arg30 as well as the side chains of Asn28, Arg30, and Arg39 through hydrogen bonds. His43 is close to the C2 carbon of FPP and may stabilize the farnesyl cation intermediate during catalysis. The hydrocarbon moiety of FPP is bound with hydrophobic amino acids including Leu85, Leu88, and Phe89, located on the alpha3 helix. The binding mode of FPP in cis-type UPPs is apparently different from that of trans-type and many other prenyltransferases which utilize Asprich motifs for substrate binding via Mg(2+). The new structure provides a plausible mechanism for the catalysis of UPPs.

  5. Alternative modes of client binding enable functional plasticity of Hsp70

    NASA Astrophysics Data System (ADS)

    Mashaghi, Alireza; Bezrukavnikov, Sergey; Minde, David P.; Wentink, Anne S.; Kityk, Roman; Zachmann-Brand, Beate; Mayer, Matthias P.; Kramer, Günter; Bukau, Bernd; Tans, Sander J.

    2016-11-01

    The Hsp70 system is a central hub of chaperone activity in all domains of life. Hsp70 performs a plethora of tasks, including folding assistance, protection against aggregation, protein trafficking, and enzyme activity regulation, and interacts with non-folded chains, as well as near-native, misfolded, and aggregated proteins. Hsp70 is thought to achieve its many physiological roles by binding peptide segments that extend from these different protein conformers within a groove that can be covered by an ATP-driven helical lid. However, it has been difficult to test directly how Hsp70 interacts with protein substrates in different stages of folding and how it affects their structure. Moreover, recent indications of diverse lid conformations in Hsp70-substrate complexes raise the possibility of additional interaction mechanisms. Addressing these issues is technically challenging, given the conformational dynamics of both chaperone and client, the transient nature of their interaction, and the involvement of co-chaperones and the ATP hydrolysis cycle. Here, using optical tweezers, we show that the bacterial Hsp70 homologue (DnaK) binds and stabilizes not only extended peptide segments, but also partially folded and near-native protein structures. The Hsp70 lid and groove act synergistically when stabilizing folded structures: stabilization is abolished when the lid is truncated and less efficient when the groove is mutated. The diversity of binding modes has important consequences: Hsp70 can both stabilize and destabilize folded structures, in a nucleotide-regulated manner; like Hsp90 and GroEL, Hsp70 can affect the late stages of protein folding; and Hsp70 can suppress aggregation by protecting partially folded structures as well as unfolded protein chains. Overall, these findings in the DnaK system indicate an extension of the Hsp70 canonical model that potentially affects a wide range of physiological roles of the Hsp70 system.

  6. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

    SciTech Connect

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; Joachimiak, Andrzej

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.

  7. Single-stranded DNA-binding proteins: multiple domains for multiple functions.

    PubMed

    Dickey, Thayne H; Altschuler, Sarah E; Wuttke, Deborah S

    2013-07-02

    The recognition of single-stranded DNA (ssDNA) is integral to myriad cellular functions. In eukaryotes, ssDNA is present stably at the ends of chromosomes and at some promoter elements. Furthermore, it is formed transiently by several cellular processes including telomere synthesis, transcription, and DNA replication, recombination, and repair. To coordinate these diverse activities, a variety of proteins have evolved to bind ssDNA in a manner specific to their function. Here, we review the recognition of ssDNA through the analysis of high-resolution structures of proteins in complex with ssDNA. This functionally diverse set of proteins arises from a limited set of structural motifs that can be modified and arranged to achieve distinct activities, including a range of ligand specificities. We also investigate the ways in which these domains interact in the context of large multidomain proteins/complexes. These comparisons reveal the structural features that define the range of functions exhibited by these proteins.

  8. A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design

    NASA Astrophysics Data System (ADS)

    Segura-Cabrera, Aldo; Bocanegra-García, Virgilio; Lizarazo-Ortega, Cristian; Guo, Xianwu; Correa-Basurto, José; Rodríguez-Pérez, Mario A.

    2011-12-01

    Onchocerciasis is a leading cause of blindness with at least 37 million people infected and more than 120 million people at risk of contracting the disease; most (99%) of this population, threatened by infection, live in Africa. The drug of choice for mass treatment is the microfilaricidal Mectizan® (ivermectin); it does not kill the adult stages of the parasite at the standard dose which is a single annual dose aimed at disease control. However, multiple treatments a year with ivermectin have effects on adult worms. The discovery of new therapeutic targets and drugs directed towards the killing of the adult parasites are thus urgently needed. The chitinase of filarial nematodes is a new drug target due to its essential function in the metabolism and molting of the parasite. Closantel is a potent and specific inhibitor of chitinase of Onchocerca volvulus (OvCHT1) and other filarial chitinases. However, the binding mode and specificity of closantel towards OvCHT1 remain unknown. In the absence of a crystallographic structure of OvCHT1, we developed a homology model of OvCHT1 using the currently available X-ray structures of human chitinases as templates. Energy minimization and molecular dynamics (MD) simulation of the model led to a high quality of 3D structure of OvCHIT1. A flexible docking study using closantel as the ligand on the binding site of OvCHIT1 and human chitinases was performed and demonstrated the differences in the closantel binding mode between OvCHIT1 and human chitinase. Furthermore, molecular dynamics simulations and free-energy calculation were employed to determine and compare the detailed binding mode of closantel with OvCHT1 and the structure of human chitinase. This comparative study allowed identification of structural features and properties responsible for differences in the computationally predicted closantel binding modes. The homology model and the closantel binding mode reported herein might help guide the rational development of

  9. Binding modes of noncompetitive GABA-channel blockers revisited using engineered affinity-labeling reactions combined with new docking studies.

    PubMed

    Charon, Sébastien; Taly, Antoine; Rodrigo, Jordi; Perret, Philippe; Goeldner, Maurice

    2011-04-13

    The binding modes of noncompetitive GABA(A)-channel blockers were re-examined taking into account the recent description of the 3D structure of prokaryotic pentameric ligand-gated ion channels, which provided access to new mammalian or insect GABA receptor models, emphasizing their transmembrane portion. Two putative binding modes were deciphered for this class of compounds, including the insecticide fipronil, located nearby either the intra- or the extracellular part of the membrane, respectively. These results are in full agreement with previously described affinity-labeling reactions performed with GABA(A) noncompetitive blockers (Perret et al. J. Biol. Chem.1999, 274, 25350-25354).

  10. Single-longitudinal-mode erbium-doped fiber laser with multiple linear cavity

    NASA Astrophysics Data System (ADS)

    Feng, Suchun; Xu, Ou; Lu, Shaohua; Ren, Wenhua; Jian, Shuisheng

    2008-12-01

    An improved stable single-longitudinal-mode (SLM) erbium-doped fiber (EDF) laser with multiple-linear short cavity is demonstrated. Three fiber Bragg gratings (FBGs) with the same parameters directly written in a homemade photosensitive EDF (PEDF) in a single step are used as the wavelength-selective and mode-selective component in a 14 cm long linear laser cavity. The optical signal-to-noise ratio (OSNR) is over 50 dB. The amplitude variation in nearly one hour is less than 0.3 dB. The proposed laser has the advantages such as simple fabrication and compact all-optical fiber configuration.

  11. Interaction of 6 Mercaptopurine with Calf Thymus DNA – Deciphering the Binding Mode and Photoinduced DNA Damage

    PubMed Central

    Rehman, Sayeed Ur; Yaseen, Zahid; Husain, Mohammed Amir; Sarwar, Tarique; Ishqi, Hassan Mubarak; Tabish, Mohammad

    2014-01-01

    DNA is one of the major intracellular targets for a wide range of anticancer and antibiotic drugs. Elucidating the binding between small molecules and DNA provides great help in understanding drug-DNA interactions and in designing of new and promising drugs for clinical use. The ability of small molecules to bind and interfere with DNA replication and transcription provides further insight into how the drugs control the expression of genes. Interaction of an antimetabolite anticancer drug 6mercaptopurine (6MP) with calf thymus DNA was studied using various approaches like UV-visible spectroscopy, fluorescence spectroscopy, CD, viscosity and molecular docking. UV-visible spectroscopy confirmed 6MP-DNA interaction. Steady state fluorescence experiments revealed a moderate binding constant of 7.48×103 M−1 which was consistent with an external binding mode. Competitive displacement assays further confirmed a non-intercalative binding mode of 6MP which was further confirmed by CD and viscosity experiments. Molecular docking further revealed the minimum energy conformation (−119.67 kJ/mole) of the complex formed between DNA and 6MP. Hence, the biophysical techniques and in-silico molecular docking approaches confirmed the groove binding/electrostatic mode of interaction between 6MP and DNA. Further, photo induced generation of ROS by 6MP was studied spectrophotometrically and DNA damage was assessed by plasmid nicking and comet assay. There was a significant increase in ROS generation and consequent DNA damage in the presence of light. PMID:24718609

  12. Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

    PubMed Central

    Felicori, Liza; Jameson, Katie H.; Roblin, Pierre; Fogg, Mark J.; Garcia-Garcia, Transito; Ventroux, Magali; Cherrier, Mickaël V.; Bazin, Alexandre; Noirot, Philippe; Wilkinson, Anthony J.; Molina, Franck; Terradot, Laurent; Noirot-Gros, Marie-Françoise

    2016-01-01

    YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell. PMID:26615189

  13. Free-standing protein films for dynamic mode detection of cations binding

    NASA Astrophysics Data System (ADS)

    Saya, Daisuke; Coleman, Anthony W.; Lazar, Adina N.; Bergaud, Christian; Nicu, Liviu

    2005-09-01

    This letter reports on the investigation of the mechano-chemical effect of cross-linked dried free-standing alpha-lactalbumin (α-lactalbumin) thin films induced by different cation, calcium, magnesium, and potassium binding. The protein membranes were fabricated by drying droplets of an α-lactalbumin solution on top of silicon through-wafer holes obtained by deep reactive ion etching. Then the membranes were consecutively exposed to solutions of the cations in HEPES buffer solution while their resonant frequencies were measured by full-field surface stroboscopic white light interferometry. Tests on more than 30 free-standing protein films showed more significant conformational changes of the α-lactalbumin after immersion in a calcium solution than those observed after immersion in magnesium and potassium solutions. These results demonstrate, the real potential of free-standing protein films to be used as resonant biosensors for multiple cation detection.

  14. Myelin Basic Protein and a Multiple Sclerosis-related MBP-peptide Bind to Oligonucleotides

    PubMed Central

    Rozenblum, Guido Tomás; Kaufman, Tomás; Vitullo, Alfredo Daniel

    2014-01-01

    Aptamer ligands for myelin basic protein (MBP) were obtained using the systematic evolution of ligand by exponential enrichment (SELEX) method. Two clones were isolated from a pool of oligonucleotides and tested for MBP targeting. Using purified MBP, we demonstrated the binding activity of the aptamers and we also showed the affinity of MBP for oligonucleotides of specific length. Moreover, one selected aptamer competitively inhibited the binding of an MBP-specific antibody to MBP and the aptamer was found more sensitive than a commercial antibody. In addition, we showed the ability of the aptamer to detect myelin-rich regions in paraffin-embedded mouse brain tissue. Therefore, the MBP-binding activity of the selected oligonucleotide may prove useful as a tool for life science and medical research for myelin detection and might be a good lead for testing it in autoimmune diseases such as multiple sclerosis. PMID:25202925

  15. Optical modes within III-nitride multiple quantum well microdisk cavities

    NASA Astrophysics Data System (ADS)

    Mair, R. A.; Zeng, K. C.; Lin, J. Y.; Jiang, H. X.; Zhang, B.; Dai, L.; Botchkarev, A.; Kim, W.; Morkoç, H.; Khan, M. A.

    1998-03-01

    Optical resonance modes have been observed in optically pumped microdisk cavities fabricated from 50 Å/50 Å GaN/AlxGa1-xN(x˜0.07) and 45 Å/45 Å InxGa1-xN/GaN(x˜0.15) multiple quantum well structures. Microdisks, approximately 9 μm in diameter and regularly spaced every 50 μm, were formed by an ion beam etch process. Individual disks were pumped at 300 and 10 K with 290 nm laser pulses focused to a spot size much smaller than the disk diameter. Optical modes corresponding to (i) the radial mode type with a spacing of 49-51 meV (both TE and TM) and (ii) the Whispering Gallery mode with a spacing of 15-16 meV were observed in the GaN microdisk cavities. The spacings of these modes are consistent with those expected for modes within a resonant cavity of cylindrical symmetry, refractive index, and dimensions of the microdisks under investigation. The GaN-based microdisk cavity is compared with its GaAs counterpart and implications regarding future GaN-based microdisk lasers are discussed.

  16. Non-Geiger mode single photon detector with multiple amplification and gain control mechanisms

    SciTech Connect

    Nawar Rahman, Samia Hall, David; Lo, Yu-Hwa

    2014-05-07

    A new type of single photon detector, Multiple Amplification Gain with Internal Control (MAGIC), is proposed and analyzed using Monte Carlo simulations based on a physical model of the device. The MAGIC detector has two coupled amplification mechanisms, avalanche multiplication and bipolar gain, and the net gain is regulated by a built-in feedback mechanism. Compared to conventional Geiger mode single photon avalanche detectors (SPADs), the MAGIC detector produces a much greater single photon detection efficiency of nearly 100%, low bit-error-ratio for single photon signals, and a large dynamic range. All these properties are highly desirable for applications that require single photon sensitivity and are absent for conventional Geiger-mode SPADs.

  17. Probing the Pairing Interaction and Multiple Bardasis-Schrieffer Modes Using Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Maiti, S.; Maier, T. A.; Böhm, T.; Hackl, R.; Hirschfeld, P. J.

    2016-12-01

    In unconventional superconductors, understanding the form of the pairing interaction is the primary goal. In this regard, Raman spectroscopy is a very useful tool, as it identifies the ground state and also the subleading pairing channels by probing collective modes. Here, we propose a general theory for a multiband Raman response and identify new features in the spectrum that can provide a robust test for a pairing theory. We identify multiple Bardasis-Schrieffer type collective modes and connect the weights of these modes to the subleading gap structures within a microscopic pairing theory. While our conclusions are completely general, we apply our approach to interpret the specific case of B1 g Raman scattering in hole-doped BaFe2 As2 .

  18. New insight into the binding modes of TNP-AMP to human liver fructose-1,6-bisphosphatase

    NASA Astrophysics Data System (ADS)

    Han, Xinya; Huang, Yunyuan; Zhang, Rui; Xiao, San; Zhu, Shuaihuan; Qin, Nian; Hong, Zongqin; Wei, Lin; Feng, Jiangtao; Ren, Yanliang; Feng, Lingling; Wan, Jian

    2016-08-01

    Human liver fructose-1,6-bisphosphatase (FBPase) contains two binding sites, a substrate fructose-1,6-bisphosphate (FBP) active site and an adenosine monophosphate (AMP) allosteric site. The FBP active site works by stabilizing the FBPase, and the allosteric site impairs the activity of FBPase through its binding of a nonsubstrate molecule. The fluorescent AMP analogue, 2‧,3‧-O-(2,4,6-trinitrophenyl)adenosine 5‧-monophosphate (TNP-AMP) has been used as a fluorescent probe as it is able to competitively inhibit AMP binding to the AMP allosteric site and, therefore, could be used for exploring the binding modes of inhibitors targeted on the allosteric site. In this study, we have re-examined the binding modes of TNP-AMP to FBPase. However, our present enzyme kinetic assays show that AMP and FBP both can reduce the fluorescence from the bound TNP-AMP through competition for FBPase, suggesting that TNP-AMP binds not only to the AMP allosteric site but also to the FBP active site. Mutagenesis assays of K274L (located in the FBP active site) show that the residue K274 is very important for TNP-AMP to bind to the active site of FBPase. The results further prove that TNP-AMP is able to bind individually to the both sites. Our present study provides a new insight into the binding mechanism of TNP-AMP to the FBPase. The TNP-AMP fluorescent probe can be used to exam the binding site of an inhibitor (the active site or the allosteric site) using FBPase saturated by AMP and FBP, respectively, or the K247L mutant FBPase.

  19. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

    PubMed Central

    Reshetnikov, Roman V.; Sponer, Jiri; Rassokhina, Olga I.; Kopylov, Alexei M.; Tsvetkov, Philipp O.; Makarov, Alexander A.; Golovin, Andrey V.

    2011-01-01

    A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange. PMID:21893589

  20. Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

    PubMed

    Reshetnikov, Roman V; Sponer, Jiri; Rassokhina, Olga I; Kopylov, Alexei M; Tsvetkov, Philipp O; Makarov, Alexander A; Golovin, Andrey V

    2011-12-01

    A combination of explicit solvent molecular dynamics simulation (30 simulations reaching 4 µs in total), hybrid quantum mechanics/molecular mechanics approach and isothermal titration calorimetry was used to investigate the atomistic picture of ion binding to 15-mer thrombin-binding quadruplex DNA (G-DNA) aptamer. Binding of ions to G-DNA is complex multiple pathway process, which is strongly affected by the type of the cation. The individual ion-binding events are substantially modulated by the connecting loops of the aptamer, which play several roles. They stabilize the molecule during time periods when the bound ions are not present, they modulate the route of the ion into the stem and they also stabilize the internal ions by closing the gates through which the ions enter the quadruplex. Using our extensive simulations, we for the first time observed full spontaneous exchange of internal cation between quadruplex molecule and bulk solvent at atomistic resolution. The simulation suggests that expulsion of the internally bound ion is correlated with initial binding of the incoming ion. The incoming ion then readily replaces the bound ion while minimizing any destabilization of the solute molecule during the exchange.

  1. The impact of embedding multiple modes of representation on student construction of chemistry knowledge

    NASA Astrophysics Data System (ADS)

    McDermott, Mark Andrew

    2009-12-01

    This study was designed to examine the impact of embedding multiple modes of representing science information on student conceptual understanding in science. Multiple representations refer to utilizing charts, graphs, diagrams, and other types of representations to communicate scientific information. This study investigated the impact of encouraging students to embed or integrate the multiple modes with text in end of unit writing-to-learn activities. A quasi-experimental design with four separate sites consisting of intact chemistry classes taught by different teachers at each site was utilized. At each site, approximately half of the classes were designated treatment classes and students in these classes participated in activities designed to encourage strategies to embed multiple modes within text in student writing. The control classes did not participate in these activities. All classes participated in identical end of unit writing tasks in which they were required to use at least one mode other than text, followed by identical end of unit assessments. This progression was then repeated for a second consecutive unit of study. Analysis of quantitative data indicated that in several cases, treatment classes significantly outperformed control classes both on measures of embeddedness in writing and on end of unit assessment measures. In addition, analysis at the level of individual students indicated significant positive correlations in many cases between measures of student embeddedness in writing and student performance on end of unit assessments. Three factors emerged as critical in increasing the likelihood of benefit for students from these types of activities. First, the level of teacher implementation and emphasis on the embeddedness lessons was linked to the possibility of conceptual benefit. Secondly, students participating in two consecutive lessons appeared to receive greater benefit during the second unit, inferring a cumulative benefit. Finally

  2. Excitation of surface plasmon polariton modes with multiple nitrogen vacancy centers in single nanodiamonds

    NASA Astrophysics Data System (ADS)

    Kumar, Shailesh; Lausen, Jens L.; Garcia-Ortiz, Cesar E.; Andersen, Sebastian K. H.; Roberts, Alexander S.; Radko, Ilya P.; Smith, Cameron L. C.; Kristensen, Anders; Bozhevolnyi, Sergey I.

    2016-02-01

    Nitrogen-vacancy (NV) centers in diamonds are interesting due to their remarkable characteristics that are well suited to applications in quantum-information processing and magnetic field sensing, as well as representing stable fluorescent sources. Multiple NV centers in nanodiamonds (NDs) are especially useful as biological fluorophores due to their chemical neutrality, brightness and room-temperature photostability. Furthermore, NDs containing multiple NV centers also have potential in high-precision magnetic field and temperature sensing. Coupling NV centers to propagating surface plasmon polariton (SPP) modes gives a base for lab-on-a-chip sensing devices, allows enhanced fluorescence emission and collection which can further enhance the precision of NV-based sensors. Here, we investigate coupling of multiple NV centers in individual NDs to the SPP modes supported by silver surfaces protected by thin dielectric layers and by gold V-grooves (VGs) produced via the self-terminated silicon etching. In the first case, we concentrate on monitoring differences in fluorescence spectra obtained from a source ND, which is illuminated by a pump laser, and from a scattering ND illuminated only by the fluorescence-excited SPP radiation. In the second case, we observe changes in the average NV lifetime when the same ND is characterized outside and inside a VG. Fluorescence emission from the VG terminations is also observed, which confirms the NV coupling to the VG-supported SPP modes.

  3. One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening†

    PubMed Central

    2009-01-01

    The enzyme pteridine reductase 1 (PTR1) is a potential target for new compounds to treat human African trypanosomiasis. A virtual screening campaign for fragments inhibiting PTR1 was carried out. Two novel chemical series were identified containing aminobenzothiazole and aminobenzimidazole scaffolds, respectively. One of the hits (2-amino-6-chloro-benzimidazole) was subjected to crystal structure analysis and a high resolution crystal structure in complex with PTR1 was obtained, confirming the predicted binding mode. However, the crystal structures of two analogues (2-amino-benzimidazole and 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole) in complex with PTR1 revealed two alternative binding modes. In these complexes, previously unobserved protein movements and water-mediated protein−ligand contacts occurred, which prohibited a correct prediction of the binding modes. On the basis of the alternative binding mode of 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole, derivatives were designed and selective PTR1 inhibitors with low nanomolar potency and favorable physicochemical properties were obtained. PMID:19527033

  4. Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode.

    PubMed

    Ricci, Clarisse G; Netz, Paulo A

    2009-08-01

    Despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. In this paper, we used AutoDock 4.0 to perform self-dockings and cross dockings between two DNA ligands (a minor groove binder and an intercalator) and four distinct receptors: 1) crystallographic DNA without intercalation gap; 2) crystallographic DNA with intercalation gap; 3) canonical B-DNA; and 4) modified B-DNA with intercalation gap. Besides being efficient in self-dockings, AutoDock is capable of correctly identifying two of the main DNA binding modes with the condition that the target possesses an artificial intercalation gap. Therefore, we suggest a default protocol to identify DNA binding modes which uses a modified canonical DNA (with gap) as receptor. This protocol was applied to dock two different Troger bases to DNA and the predicted binding modes agree with those suggested, yet not established, by experimental data. We also applied the protocol to dock aflatoxin B(1) exo-8,9-epoxide, and the results are in complete agreement with experimental data from the literature. We propose that this approach can be used to investigate other ligands whose binding mode to DNA remains unknown, yielding a suitable starting point for further theoretical studies such as molecular dynamics simulations.

  5. Discovery of a Potent BTK Inhibitor with a Novel Binding Mode by Using Parallel Selections with a DNA-Encoded Chemical Library.

    PubMed

    Cuozzo, John W; Centrella, Paolo A; Gikunju, Diana; Habeshian, Sevan; Hupp, Christopher D; Keefe, Anthony D; Sigel, Eric A; Soutter, Holly H; Thomson, Heather A; Zhang, Ying; Clark, Matthew A

    2017-01-05

    We have identified and characterized novel potent inhibitors of Bruton's tyrosine kinase (BTK) from a single DNA-encoded library of over 110 million compounds by using multiple parallel selection conditions, including variation in target concentration and addition of known binders to provide competition information. Distinct binding profiles were observed by comparing enrichments of library building block combinations under these conditions; one enriched only at high concentrations of BTK and was competitive with ATP, and another enriched at both high and low concentrations of BTK and was not competitive with ATP. A compound representing the latter profile showed low nanomolar potency in biochemical and cellular BTK assays. Results from kinetic mechanism of action studies were consistent with the selection profiles. Analysis of the co-crystal structure of the most potent compound demonstrated a novel binding mode that revealed a new pocket in BTK. Our results demonstrate that profile-based selection strategies using DNA-encoded libraries form the basis of a new methodology to rapidly identify small molecule inhibitors with novel binding modes to clinically relevant targets.

  6. Amyloid tracers detect multiple binding sites in Alzheimer's disease brain tissue.

    PubMed

    Ni, Ruiqing; Gillberg, Per-Göran; Bergfors, Assar; Marutle, Amelia; Nordberg, Agneta

    2013-07-01

    -1 (Ki: 0.2 nM, 70 nM), florbetapir (1.8 nM, 53 nM) and florbetaben (1.0 nM, 65 nM). BF-227 displaced 83% of (3)H-Pittsburgh compound B binding, mainly at a low-affinity site (311 nM), whereas FDDNP only partly displaced (40%). We propose a multiple binding site model for the amyloid tracers (binding sites 1, 2 and 3), where AV-45 (florbetapir), AV-1 (florbetaben), and Pittsburgh compound B, all show nanomolar affinity for the high-affinity site (binding site 1), as visualized by positron emission tomography. BF-227 shows mainly binding to site 3 and FDDNP shows only some binding to site 2. Different amyloid tracers may provide new insight into the pathophysiological mechanisms in the progression of Alzheimer's disease.

  7. 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.

    PubMed

    Paoletti, Julie; Assairi, Liliane; Gelin, Muriel; Huteau, Valérie; Nahori, Marie-Anne; Dussurget, Olivier; Labesse, Gilles; Pochet, Sylvie

    2016-11-29

    Increased resistance of pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials. Biosynthetic pathways of several cofactors important for bacterial growth, such as nicotinamide adenine dinucleotide phosphate (NADP), have been proposed as a promising source of antibiotic targets. Nicotinamide adenine dinucleotide kinases (NADK; EC 2.7.1.23) are attractive for inhibitor development, since they catalyze the phosphorylation of NAD to NADP, which is an essential step of NADP metabolism. We previously synthesized diadenosine derivatives that inhibited NADK from two human pathogens, Listeria monocytogenes and Staphylococcus aureus, in the micromolar range. They behave as NAD mimics with the 5',5'-diphosphate group substituted by a 8,5' thioglycolic bridge. In an attempt to improve inhibitory potency, we designed new NAD mimics based on a single adenosine moiety harboring a larger derivatization attached to the C8 position and a small group at the 5' position. Here we report the synthesis of a series of 8-thioalkyl-adenosine derivatives containing various aryl and heteroaryl moieties and their evaluation as inhibitors of L. monocytogenes NADK1, S. aureus NADK and their human counterpart. Novel, sub-micromolar inhibitors of LmNADK1 were identified. Surprisingly, most LmNADK1 inhibitors demonstrated a high selectivity index against the close staphylococcal ortholog and the human NADK. Structural characterization of enzyme-inhibitor complexes revealed the original binding mode of these novel NAD mimics.

  8. Structural basis of constitutive activity and a unique nucleotide binding mode of human Pim-1 kinase.

    PubMed

    Qian, Kevin C; Wang, Lian; Hickey, Eugene R; Studts, Joey; Barringer, Kevin; Peng, Charline; Kronkaitis, Anthony; Li, Jun; White, Andre; Mische, Sheenah; Farmer, Bennett

    2005-02-18

    Pim-1 kinase is a member of a distinct class of serine/threonine kinases consisting of Pim-1, Pim-2, and Pim-3. Pim kinases are highly homologous to one another and share a unique consensus hinge region sequence, ER-PXPX, with its two proline residues separated by a non-conserved residue, but they (Pim kinases) have <30% sequence identity with other kinases. Pim-1 has been implicated in both cytokine-induced signal transduction and the development of lymphoid malignancies. We have determined the crystal structures of apo Pim-1 kinase and its AMP-PNP (5'-adenylyl-beta,gamma-imidodiphosphate) complex to 2.1-angstroms resolutions. The structures reveal the following. 1) The kinase adopts a constitutively active conformation, and extensive hydrophobic and hydrogen bond interactions between the activation loop and the catalytic loop might be the structural basis for maintaining such a conformation. 2) The hinge region has a novel architecture and hydrogen-bonding pattern, which not only expand the ATP pocket but also serve to establish unambiguously the alignment of the Pim-1 hinge region with that of other kinases. 3) The binding mode of AMP-PNP to Pim-1 kinase is unique and does not involve a critical hinge region hydrogen bond interaction. Analysis of the reported Pim-1 kinase-domain structures leads to a hypothesis as to how Pim kinase activity might be regulated in vivo.

  9. Ruthenium complexes of substituted hydrazine: new solution- and solid-state binding modes.

    PubMed

    Dabb, Serin L; Messerle, Barbara A; Otting, Gottfried; Wagler, Jörg; Willis, Anthony

    2008-01-01

    The methylhydrazine complex [Ru(NH(2)NHMe)(PyP)(2)]Cl(BPh(4)) (PyP=1-[2-(diphenylphosphino)ethyl]pyrazole) was synthesised by addition of methylhydrazine to the bimetallic complex [Ru(mu-Cl)(PyP)(2)](2)(BPh(4))(2). The methylhydrazine ligand of the ruthenium complex has two different binding modes: side-on (eta(2)-) when the complex is in the solid state and end-on (eta(1)-) when the complex is in solution. The solid-state structure of [Ru(PyP)(2)(NH(2)NHMe)]Cl(BPh(4)) was determined by X-ray crystallography. 2D NMR spectroscopic experiments with (15)N at natural abundance confirmed that in solution the methylhydrazine is bound to the metal centre by only the -NH(2) group and the ruthenium complex retains an octahedral conformation. Hydrazine complexes [RuCl(PyP)(2)(eta(1)-NH(2)NRR')]OSO(2)CF(3) (in which R=H, R'=Ph, R=R'=Me and NRR'=NC(5)H(10)) were formed in situ by the addition of phenylhydrazine, 1,1-dimethylhydrazine and N-aminopiperidine, respectively, to a solution of the bimetallic complex [Ru(mu-Cl)(PyP)(2)](2)(OSO(2)CF(3))(2) in dichloromethane. These substituted hydrazine complexes of ruthenium were shown to exist in an equilibrium mixture with the bimetallic starting material.

  10. A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC

    SciTech Connect

    Sethi, D.K.; Heroux, A.; Schubert, D. A.; Anders, A.-K.; Bonsor, D. A.; Thomas, C. P.; Sundberg, E. J.; Pyrdol, J.; Wucherpfennig, K. W.

    2011-01-17

    Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-{alpha} chain with the MHC class II {beta} chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3{beta} loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3{alpha} loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.

  11. A Highly Tilted Binding Mode by a Self-Reactive T Cell Receptor Results in Altered Engagement of Peptide and MHC

    SciTech Connect

    D Sethi; D Schubert; A Anders; A Heroux; D Bonsor; C Thomas; E Sundberg; J Pyrdol; K Wucherpfennig

    2011-12-31

    Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide-major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-{alpha} chain with the MHC class II {beta} chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3{beta} loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3{alpha} loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.

  12. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode.

    PubMed

    Stanek, Kimberly A; Patterson-West, Jennifer; Randolph, Peter S; Mura, Cameron

    2017-04-01

    The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

  13. Dynamic binding of identity and location information: a serial model of multiple identity tracking.

    PubMed

    Oksama, Lauri; Hyönä, Jukka

    2008-06-01

    Tracking of multiple moving objects is commonly assumed to be carried out by a fixed-capacity parallel mechanism. The present study proposes a serial model (MOMIT) to explain performance accuracy in the maintenance of multiple moving objects with distinct identities. A serial refresh mechanism is postulated, which makes recourse to continuous attention switching, a capacity-limited episodic buffer for identity-location bindings, indexed location information stored in the visuospatial short-term memory, and an active role of long-term memory. As identity-location bindings are refreshed serially, a location error is inherent for all other targets except the focally attended one. The magnitude of this location error is a key factor in predicting tracking accuracy. MOMIT's predictions were supported by the data of five experiments: performance accuracy decreased as a function of target set-size, speed, and familiarity. A mathematical version of MOMIT fitted nicely to the observed data with plausible parameter estimates for the binding capacity and refresh time.

  14. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    NASA Astrophysics Data System (ADS)

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; Lehoux, Jean-Guy; Lavigne, Pierre

    2016-06-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

  15. Multiple binding sites in the nicotinic acetylcholine receptors: An opportunity for polypharmacolgy.

    PubMed

    Iturriaga-Vásquez, Patricio; Alzate-Morales, Jans; Bermudez, Isabel; Varas, Rodrigo; Reyes-Parada, Miguel

    2015-11-01

    For decades, the development of selective compounds has been the main goal for chemists and biologists involved in drug discovery. However, diverse lines of evidence indicate that polypharmacological agents, i.e. those that act simultaneously at various protein targets, might show better profiles than selective ligands, regarding both efficacy and side effects. On the other hand, the availability of the crystal structure of different receptors allows a detailed analysis of the main interactions between drugs and receptors in a specific binding site. Neuronal nicotinic acetylcholine receptors (nAChRs) constitute a large and diverse family of ligand-gated ion channels (LGICs) that, as a product of its modulation, regulate neurotransmitter release, which in turns produce a global neuromodulation of the central nervous system. nAChRs are pentameric protein complexes in such a way that expression of compatible subunits can lead to various receptor assemblies or subtypes. The agonist binding site, located at the extracellular region, exhibits different properties depending on the subunits that conform the receptor. In the last years, it has been recognized that nAChRs could also contain one or more allosteric sites which could bind non-classical nicotinic ligands including several therapeutically useful drugs. The presence of multiple binding sites in nAChRs offers an interesting possibility for the development of novel polypharmacological agents with a wide spectrum of actions.

  16. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    PubMed Central

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; LeHoux, Jean-Guy; Lavigne, Pierre

    2016-01-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6. PMID:27340016

  17. Engineering Factor Xa Inhibitor with Multiple Platelet-Binding Sites Facilitates its Platelet Targeting

    NASA Astrophysics Data System (ADS)

    Zhu, Yuanjun; Li, Ruyi; Lin, Yuan; Shui, Mengyang; Liu, Xiaoyan; Chen, Huan; Wang, Yinye

    2016-07-01

    Targeted delivery of antithrombotic drugs centralizes the effects in the thrombosis site and reduces the hemorrhage side effects in uninjured vessels. We have recently reported that the platelet-targeting factor Xa (FXa) inhibitors, constructed by engineering one Arg-Gly-Asp (RGD) motif into Ancylostoma caninum anticoagulant peptide 5 (AcAP5), can reduce the risk of systemic bleeding than non-targeted AcAP5 in mouse arterial injury model. Increasing the number of platelet-binding sites of FXa inhibitors may facilitate their adhesion to activated platelets, and further lower the bleeding risks. For this purpose, we introduced three RGD motifs into AcAP5 to generate a variant NR4 containing three platelet-binding sites. NR4 reserved its inherent anti-FXa activity. Protein-protein docking showed that all three RGD motifs were capable of binding to platelet receptor αIIbβ3. Molecular dynamics simulation demonstrated that NR4 has more opportunities to interact with αIIbβ3 than single-RGD-containing NR3. Flow cytometry analysis and rat arterial thrombosis model further confirmed that NR4 possesses enhanced platelet targeting activity. Moreover, NR4-treated mice showed a trend toward less tail bleeding time than NR3-treated mice in carotid artery endothelium injury model. Therefore, our data suggest that engineering multiple binding sites in one recombinant protein is a useful tool to improve its platelet-targeting efficiency.

  18. Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft.

    PubMed

    Showalter, Scott A; Bruschweiler-Li, Lei; Johnson, Eric; Zhang, Fengli; Brüschweiler, Rafael

    2008-05-21

    The oncoprotein MDM2 regulates the activity and stability of the tumor suppressor p53 through protein-protein interaction involving their N-terminal domains. The N-terminal lid of MDM2 has been implicated in p53 regulation; however, due to its flexible nature, limited data are available concerning its role in ligand binding. The quantitative dynamics study using NMR reported here shows, for the first time, that the lid in apo-MDM2 slowly interconverts between a "closed" state that is associated with the p53-binding cleft and an "open" state that is highly flexible. Our results reveal that apo-MDM2 predominantly populates the closed state, whereas the p53-bound MDM2 exclusively populates the open state. Unlike p53 binding, the small molecule MDM2 antagonist nutlin-3 binds to the cleft essentially without perturbing the closed lid state. The lid dynamics thereby represents a signature for the experimental and virtual screening of therapeutic antagonists that target the p53-MDM2 interaction.

  19. Interactions of multiple predators with different foraging modes in an aquatic food web.

    PubMed

    Carey, Michael P; Wahl, David H

    2010-02-01

    Top predators can have different foraging modes that may alter their interactions and effects on food webs. Interactions between predators may be non-additive resulting from facilitation or interference, whereas their combined effects on a shared prey may result in emergent effects that are risk enhanced or risk reduced. To test the importance of multiple predators with different foraging modes, we examined the interaction between a cruising predator (largemouth bass, Micropterus salmoides) and an ambush predator (muskellunge, Esox masquinongy) foraging on a shared prey (bluegill sunfish, Lepomis macrochirus) with strong anti-predator defense behaviors. Additive and substitution designs were used to compare individual to combined predator treatments in experimental ponds. The multiple predator interaction facilitated growth of the cruising predator in the combined predator treatments, whereas predator species had substitutable effects on the growth of the ambush predator. The combined predator treatments created an emergent effect on the prey; however, the direction was dependent on the experimental design. The additive design found a risk-reducing effect, whereas the substitution design found a risk-enhancing effect for prey fish. Indirect effects from the predators weakly extended to lower trophic levels (i.e., zooplankton community). Our results highlight the need to consider differences in foraging mode of top predators, interactions between predators, and emergent effects on prey to understand food webs.

  20. Properties of a novel linear sulfur response mode in a multiple flame photometric detector.

    PubMed

    Clark, Adrian G; Thurbide, Kevin B

    2014-01-24

    A new linear sulfur response mode was established in the multiple flame photometric detector (mFPD) by monitoring HSO* emission in the red spectral region above 600nm. Optimal conditions for this mode were found by using a 750nm interference filter and oxygen flows to the worker flames of this device that were about 10mL/min larger than those used for monitoring quadratic S2* emission. By employing these parameters, this mode provided a linear response over about 4 orders of magnitude, with a detection limit near 5.8×10(-11)gS/s and a selectivity of sulfur over carbon of about 3.5×10(3). Specifically, the minimum detectable masses for 10 different sulfur analytes investigated ranged from 0.4 to 3.6ng for peak half-widths spanning 4-6s. The response toward ten different sulfur compounds was examined and produced an average reproducibility of 1.7% RSD (n=10) and an average equimolarity value of 1.0±0.1. In contrast to this, a conventional single flame S2* mode comparatively yielded respective values of 6.7% RSD (n=10) and 1.1±0.4. HSO* emission in the mFPD was also found to be relatively much less affected by response quenching due to hydrocarbons compared to a conventional single flame S2* emission mode. Results indicate that this new alternative linear mFPD response mode could be beneficial for sulfur monitoring applications.

  1. Selective Monocationic Inhibitors of Neuronal Nitric Oxide Synthase. Binding Mode Insights from Molecular Dynamics Simulations

    PubMed Central

    Huang, He; Ji, Haitao; Li, Huiying; Jing, Qing; Labby, Kristin Jansen; Martásek, Pavel; Roman, Linda J.; Poulos, Thomas L.; Silverman, Richard B.

    2012-01-01

    The reduction of pathophysiologic levels of nitric oxide through inhibition of neuronal nitric oxide synthase (nNOS) has the potential to be therapeutically beneficial in various neurodegenerative diseases. We have developed a series of pyrrolidine-based nNOS inhibitors that exhibit excellent potencies and isoform selectivities (J. Am. Chem. Soc. 2010, 132, 5437). However, there are still important challenges, such as how to decrease the multiple positive charges derived from basic amino groups, which contribute to poor bioavailability, without losing potency and/or selectivity. Here we present an interdisciplinary study combining molecular docking, crystallography, molecular dynamics simulations, synthesis, and enzymology to explore potential pharmacophoric features of nNOS inhibitors and to design potent and selective monocationic nNOS inhibitors. The simulation results indicate that different hydrogen bond patterns, electrostatic interactions, hydrophobic interactions, and a water molecule bridge are key factors for stabilizing ligands and controlling ligand orientation. We find that a heteroatom in the aromatic head or linker chain of the ligand provides additional stability and blocks the substrate binding pocket. Finally, the computational insights are experimentally validated with double-headed pyridine analogs. The compounds reported here are among the most potent and selective monocationic pyrrolidine-based nNOS inhibitors reported to date, and 10 shows improved membrane permeability. PMID:22731813

  2. Multiple magnetic mode-based Fano resonance in split-ring resonator/disk nanocavities.

    PubMed

    Zhang, Qing; Wen, Xinglin; Li, Guangyuan; Ruan, Qifeng; Wang, Jianfang; Xiong, Qihua

    2013-12-23

    Plasmonic Fano resonance, enabled by the weak interaction between a bright super-radiant and a subradiant resonance mode, not only is fundamentally interesting, but also exhibits potential applications ranging from extraordinary optical transmission to biosensing. Here, we demonstrate strong Fano resonances in split-ring resonators/disk (SRR/D) nanocavities. The high-order magnetic modes are observed in SRRs by polarization-resolved transmission spectroscopy. When a disk is centered within the SRRs, multiple high-order magnetic modes are coupled to a broad electric dipole mode of SRR/D, leading to significant Fano resonance spectral features in near-IR regime. The strength and line shape of the Fano resonances are tuned through varying the SRR split-angle and interparticle distance between SRR and disk. Finite-difference-time-domain (FDTD) simulations are conducted to understand the coupling mechanism, and the results show good agreement with experimental data. Furthermore, the coupled structure gives a sensitivity of ∼282 nm/RIU with a figure of merit ∼4.

  3. Stokes-space analysis of modal dispersion in fibers with multiple mode transmission.

    PubMed

    Antonelli, Cristian; Mecozzi, Antonio; Shtaif, Mark; Winzer, Peter J

    2012-05-21

    Modal dispersion (MD) in a multimode fiber may be considered as a generalized form of polarization mode dispersion (PMD) in single mode fibers. Using this analogy, we extend the formalism developed for PMD to characterize MD in fibers with multiple spatial modes. We introduce a MD vector defined in a D-dimensional extended Stokes space whose square length is the sum of the square group delays of the generalized principal states. For strong mode coupling, the MD vector undertakes a D-dimensional isotropic random walk, so that the distribution of its length is a chi distribution with D degrees of freedom. We also characterize the largest differential group delay, that is the difference between the delays of the fastest and the slowest principal states, and show that it too is very well approximated by a chi distribution, although in general with a smaller number of degrees of freedom. Finally, we study the spectral properties of MD in terms of the frequency autocorrelation functions of the MD vector, of the square modulus of the MD vector, and of the largest differential group delay. The analytical results are supported by extensive numerical simulations.

  4. Simultaneous dispersion measurements of multiple fiber modes using virtual reference interferometry.

    PubMed

    Galle, Michael A; Saini, Simarjeet S; Mohammed, Waleed S; Sillard, Pierre; Qian, Li

    2014-03-24

    We present the simultaneous measurement of first and second order dispersion in short length (< 1 m) few mode fibers (polarization and transverse) using virtual reference interferometry. This technique generates results equivalent to balanced spectral interferometry, without the complexity associated with physical balancing. This is achieved by simulating a virtual reference with a group delay equal to that of the physical interferometer. The amplitude modulation that results from mixing the interferograms, generated in both the unbalanced interferometer and the virtual reference, is equivalent to the first order interference that would be produced by physical balancing. The advantages of the technique include speed, simplicity, convenience and the capability for simultaneous measurement of multiple modes. The theoretical framework is first developed and then verified experimentally.

  5. Position synchronised control of multiple robotic manipulators based on integral sliding mode

    NASA Astrophysics Data System (ADS)

    Zhao, Dongya; Zhu, Quanmin

    2014-03-01

    In this study, a new position synchronised control algorithm is developed for multiple robotic manipulator systems. In the merit of system synchronisation and integral sliding mode control, the proposed approach can stabilise position tracking of each robotic manipulator while coordinating its motion with the other manipulators. With the integral sliding mode, the proposed approach has insensitiveness against the lumped system uncertainty within the entire process of operation. Further, a perturbation estimator is proposed to reduce chattering effect. The corresponding stability analysis is presented to lay a foundation for theoretical understanding to the underlying issues as well as safely operating real systems. An illustrative example is bench tested to validate the effectiveness of the proposed approach.

  6. Determining the binding mode and binding affinity constant of tyrosine kinase inhibitor PD153035 to DNA using optical tweezers

    SciTech Connect

    Cheng, Chih-Ming; Lee, Yuarn-Jang; Wang, Wei-Ting; Hsu, Chien-Ting; Tsai, Jing-Shin; Wu, Chien-Ming; Ou, Keng-Liang; and others

    2011-01-07

    Research highlights: {yields} PD153035 is a DNA intercalator and intercalation occurs only under very low salt concentration. {yields} The minimum distance between adjacent bound PD153035 {approx} 11 bp. {yields} Binding affinity constant for PD153035 is 1.18({+-}0.09) x 10{sup 4} (1/M). {yields} The change of binding free energy of PD153035-DNA interaction is -5.49 kcal mol{sup -1} at 23 {+-} 0.5 {sup o}C. -- Abstract: Accurately predicting binding affinity constant (K{sub A}) is highly required to determine the binding energetics of the driving forces in drug-DNA interactions. Recently, PD153035, brominated anilinoquinazoline, has been reported to be not only a highly selective inhibitor of epidermal growth factor receptor but also a DNA intercalator. Here, we use a dual-trap optical tweezers to determining K{sub A} for PD153035, where K{sub A} is determined from the changes in B-form contour length (L) of PD153035-DNA complex. Here, L is fitted using a modified wormlike chain model. We found that a noticeable increment in L in 1 mM sodium cacodylate was exhibited. Furthermore, our results showed that K{sub A} = 1.18({+-}0.09) x 10{sup 4} (1/M) at 23 {+-} 0.5 {sup o}C and the minimum distance between adjacent bound PD153035 {approx} 11 bp. We anticipate that by using this approach we can determine the complete thermodynamic profiles due to the presence of DNA intercalators.

  7. Isolation and characterization of the DNA-binding protein (DBP) of the Autographa californica multiple nucleopolyhedrovirus

    SciTech Connect

    Mikhailov, Victor S. Vanarsdall, Adam L.; Rohrmann, George F.

    2008-01-20

    DNA-binding protein (DBP) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) was expressed as an N-terminal His{sub 6}-tag fusion using a recombinant baculovirus and purified to near homogeneity. Purified DBP formed oligomers that were crosslinked by redox reagents resulting in predominantly protein dimers and tetramers. In gel retardation assays, DBP showed a high affinity for single-stranded oligonucleotides and was able to compete with another baculovirus SSB protein, LEF-3, for binding sites. DBP binding protected ssDNA against hydrolysis by a baculovirus alkaline nuclease AN/LEF-3 complex. Partial proteolysis by trypsin revealed a domain structure of DBP that is required for interaction with DNA and that can be disrupted by thermal treatment. Binding to ssDNA, but not to dsDNA, changed the pattern of proteolytic fragments of DBP indicating adjustments in protein structure upon interaction with ssDNA. DBP was capable of unwinding short DNA duplexes and also promoted the renaturation of long complementary strands of ssDNA into duplexes. The unwinding and renaturation activities of DBP, as well as the DNA binding activity, were sensitive to sulfhydryl reagents and were inhibited by oxidation of thiol groups with diamide or by alkylation with N-ethylmaleimide. A high affinity of DBP for ssDNA and its unwinding and renaturation activities confirmed identification of DBP as a member of the SSB/recombinase family. These activities and a tight association with subnuclear structures suggests that DBP is a component of the virogenic stroma that is involved in the processing of replicative intermediates.

  8. Multiple Observing Modes for Wide-field Optical Surveillance of GEO Space

    NASA Astrophysics Data System (ADS)

    McGraw, J.; Zimmer, P.; Ackermann, M.

    2016-09-01

    Very wide field of view optical sensors with silicon detectors are being used in multiple survey modes by J. T. McGraw and Associates to provide persistent, affordable surveillance of GEO space to faint limiting magnitudes. Examples include:

  9. classical staring mode with typical integration times of seconds provided by multiple co-directed sensors to provide a deep mosaic of tens of square degrees per exposure to faint limiting magnitude
  10. b) step-and-stare observations of several second integration time from which a continuous, overlapped, mosaicked image of GEO space can be provided
  11. time-delay and integrate (TDI) imagery obtained by driving the telescope in declination and stepping the telescope in the E-W direction, which produces repeated, overlapping (if desired), synoptic images of GEO space.
  12. With current 350 mm diameter optics, detection limits for concentrated observations (e.g. "neighborhood watch") detection limits of magnitude 18 are achieved, and for uncued survey the detection limits are fainter than magnitude 16. Each of these techniques can employ multiple telescopes to obtain search rates in excess of 1000 square degrees per hour, allowing complete uncued CONUS GEO surveillance to +/- 15 degrees latitude every two nighttime hours. With appropriate placement, sensors could provide complete coverage of GEO to these limiting magnitudes at the same survey rate. At each step of the development of this unique capability we discuss the fundamental underlying physical principals of optics, detectors, search modes and siting that enable this survey, a valuable adjunct to RF, radar, GEODSS and other optical surveys of GEO space.

  13. Quest for the binding mode of malachite green with humic acid

    NASA Astrophysics Data System (ADS)

    Zhang, Hongmei; Yin, Mingxing; Shi, Jinghua; Wang, Yanqing

    2015-02-01

    The association of malachite green (MG) with humic acid (HA) was investigated by using fluorescence, UV-vis spectroscopy and molecular Modelling method. The fluorescence spectral results indicated that the binding between MG and HA occurred by mainly hydrophobic and electrostatic forces with association constants of KA (298 K) = 6.24 × 105 L/mol and KA (310 K) = 10.20 × 105 L/mol. There were more than one binding sites on HA to bind with MG. The binding sites of MG with HA primarily located at the aromatic rings of HA. MG could enter into the hydrophobic cavities of HA to quench the fluorescence of HA. On the contrary, HA binding caused MG to a coplanar conformation with more extended π bond distribution by π-π stacking interactions. The experiment and calculation data both showed that the hydrophobic binding cavities in HA played a key role in its binding with MG.

  14. Parameterization of Natural Modes of Composite Rotating Conical Shells with Multiple Delamination

    NASA Astrophysics Data System (ADS)

    Dey, Sudip; Karmakar, Amit

    2012-01-01

    This paper describes a comparative study on free vibration of bending stiff, torsion stiff and quasi-isotropic graphite-epoxy composite conical shells with single and multiple delamination. The finite element formulation is based on Mindlin's theory and multi-point constraint algorithm neglecting the Coriolis effect for moderate rotational speeds. Computer codes are developed employing QR iteration method to obtain delaminated natural frequencies under combined effect of twist and rotation. Mode shapes are depicted for a typical laminate configuration. The non-dimensional natural frequencies obtained are the first known results which could serve as reference solutions for future investigators.

  15. Interference fringes in multiple Bragg-Laue mode and mirage fringes from bent crystals.

    PubMed

    Fukamachi, Tomoe; Tohyama, Masahiko; Hirano, Kenji; Yoshizawa, Masami; Negishi, Riichirou; Ju, Dongying; Hirano, Keiichi; Kawamura, Takaaki

    2010-05-01

    Interference fringes are measured in the diffraction from the surface as well as from the lateral surface of an Si single-crystal strip which is deformed in cantilever bending as a function of the tip displacement. The interference fringes are observed only when the bending strain is applied. Both interference fringes change conspicuously by increasing the bending strain. The number of the interference fringes changes, and the positions and heights of the peaks in the fringes change. These variations can be explained by the change of the interference between the beams in multiple Bragg-Laue modes and those of mirage diffraction based on the dynamical theory of diffraction.

  16. Origin of the damage ring pattern in fused silica induced by multiple longitudinal modes laser pulses

    NASA Astrophysics Data System (ADS)

    Chambonneau, M.; Diaz, R.; Grua, P.; Rullier, J.-L.; Duchateau, G.; Natoli, J.-Y.; Lamaignère, L.

    2014-01-01

    Ring patterns surrounding laser damage sites at the exit surface of fused silica are systematically observed when initiated by multiple longitudinal modes nanosecond laser pulses at 1064 nm. The appearance chronology of rings is found to be closely related to the temporal shape of the laser pulses. This supports that the damage morphology originates from the coupling of a laser-supported detonation wave propagating in air with an ablation mechanism in silica. In our experiments, the propagation speed of the detonation wave reaches about 20 km/s and scales as the cube root of the laser intensity, in good agreement with theory.

  17. Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition

    SciTech Connect

    Sigalov, Alexander B.; Hendricks, Gregory M.

    2009-11-13

    Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including {zeta}{sub cyt} and CD3{epsilon}{sub cyt} all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of {zeta}{sub cyt} and CD3{epsilon}{sub cyt} to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for {zeta}{sub cyt} and CD3{epsilon}{sub cyt} depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

  18. Mutant p53 proteins bind DNA in a DNA structure-selective mode

    PubMed Central

    Göhler, Thomas; Jäger, Stefan; Warnecke, Gabriele; Yasuda, Hideyo; Kim, Ella; Deppert, Wolfgang

    2005-01-01

    Despite the loss of sequence-specific DNA binding, mutant p53 (mutp53) proteins can induce or repress transcription of mutp53-specific target genes. To date, the molecular basis for transcriptional modulation by mutp53 is not understood, but increasing evidence points to the possibility that specific interactions of mutp53 with DNA play an important role. So far, the lack of a common denominator for mutp53 DNA binding, i.e. the existence of common sequence elements, has hampered further characterization of mutp53 DNA binding. Emanating from our previous discovery that DNA structure is an important determinant of wild-type p53 (wtp53) DNA binding, we analyzed the binding of various mutp53 proteins to oligonucleotides mimicking non-B DNA structures. Using various DNA-binding assays we show that mutp53 proteins bind selectively and with high affinity to non-B DNA. In contrast to sequence-specific and DNA structure-dependent binding of wtp53, mutp53 DNA binding to non-B DNA is solely dependent on the stereo-specific configuration of the DNA, and not on DNA sequence. We propose that DNA structure-selective binding of mutp53 proteins is the basis for the well-documented interaction of mutp53 with MAR elements and for transcriptional activities mediates by mutp53. PMID:15722483

  19. dCaP: detecting differential binding events in multiple conditions and proteins

    PubMed Central

    2014-01-01

    Background Current ChIP-seq studies are interested in comparing multiple epigenetic profiles across several cell types and tissues simultaneously for studying constitutive and differential regulation. Simultaneous analysis of multiple epigenetic features in many samples can gain substantial power and specificity than analyzing individual features and/or samples separately. Yet there are currently few tools can perform joint inference of constitutive and differential regulation in multi-feature-multi-condition contexts with statistical testing. Existing tools either test regulatory variation for one factor in multiple samples at a time, or for multiple factors in one or two samples. Many of them only identify binary rather than quantitative variation, which are sensitive to threshold choices. Results We propose a novel and powerful method called dCaP for simultaneously detecting constitutive and differential regulation of multiple epigenetic factors in multiple samples. Using simulation, we demonstrate the superior power of dCaP compared to existing methods. We then apply dCaP to two datasets from human and mouse ENCODE projects to demonstrate its utility. We show in the human dataset that the cell-type specific regulatory loci detected by dCaP are significantly enriched near genes with cell-type specific functions and disease relevance. We further show in the mouse dataset that dCaP captures genomic regions showing significant signal variations for TAL1 occupancy between two mouse erythroid cell lines. The novel TAL1 occupancy loci detected only by dCaP are highly enriched with GATA1 occupancy and differential gene expression, while those detected only by other methods are not. Conclusions Here, we developed a novel approach to utilize the cooperative property of proteins to detect differential binding given multivariate ChIP-seq samples to provide better power, aiming for complementing existing approaches and providing new insights in the method development in

  20. RNA synthesis is associated with multiple TBP-chromatin binding events

    PubMed Central

    Zaidi, Hussain A.; Auble, David T.; Bekiranov, Stefan

    2017-01-01

    Competition ChIP is an experimental method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a genome. We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction rate theory and are able to derive the physical half-life or residence time for TATA-binding protein (TBP) across the yeast genome from competition ChIP data. Using our physical modeling approach where we explicitly include the induction profile of the competitor in the model, we are able to estimate yeast TBP-chromatin residence times as short as 1.3 minutes, demonstrating that competition ChIP is a relatively high temporal-resolution approach. Strikingly, we find a median value of ~5 TBP-chromatin binding events associated with the synthesis of one RNA molecule across Pol II genes, suggesting multiple rounds of pre-initiation complex assembly and disassembly before productive elongation of Pol II is achieved at most genes in the yeast genome. PMID:28051102

  21. ESCRT-0 assembles as a heterotetrameric complex on membranes and binds multiple ubiquitinylated cargoes simultaneously.

    PubMed

    Mayers, Jonathan R; Fyfe, Ian; Schuh, Amber L; Chapman, Edwin R; Edwardson, J Michael; Audhya, Anjon

    2011-03-18

    The ESCRT machinery consists of multiple protein complexes that collectively participate in the biogenesis of multivesicular endosomes (MVEs). The ESCRT-0 complex is composed of two subunits, Hrs and STAM, both of which can engage ubiquitinylated substrates destined for lysosomal degradation. Here, we conduct a comprehensive analysis of ESCRT-0:ubiquitin interactions using isothermal titration calorimetry and define the affinity of each ubiquitin-binding domain (UBD) within the intact ESCRT-0 complex. Our data demonstrate that ubiquitin binding is non-cooperative between the ESCRT-0 UBDs. Additionally, our findings show that the affinity of the Hrs double ubiquitin interacting motif (DUIM) for ubiquitin is more than 2-fold greater than that of UBDs found in STAM, suggesting that Hrs functions as the major ubiquitin-binding protein in ESCRT-0. In vivo, Hrs and STAM localize to endosomal membranes. To study recombinant ESCRT-0 assembly on lipid bilayers, we used atomic force microscopy. Our data show that ESCRT-0 forms mostly heterodimers and heterotetramers of Hrs and STAM when analyzed in the presence of membranes. Consistent with these findings, hydrodynamic analysis of endogenous ESCRT-0 indicates that it exists largely as a heterotetrameric complex of its two subunits. Based on these data, we present a revised model for ESCRT-0 function in cargo recruitment and concentration at the endosome.

  22. Nucleobindin 1 binds to multiple types of pre-fibrillar amyloid and inhibits fibrillization

    PubMed Central

    Bonito-Oliva, Alessandra; Barbash, Shahar; Sakmar, Thomas P.; Graham, W Vallen

    2017-01-01

    During amyloid fibril formation, amyloidogenic polypeptides misfold and self assemble into soluble pre-fibrillar aggregates, i.e., protofibrils, which elongate and mature into insoluble fibrillar aggregates. An emerging class of chaperones, chaperone-like amyloid binding proteins (CLABPs), has been shown to interfere with aggregation of particular misfolded amyloid peptides or proteins. We have discovered that the calcium-binding protein nuclebindin-1 (NUCB1) is a novel CLABP. We show that NUCB1 inhibits aggregation of islet-amyloid polypeptide associated with type 2 diabetes mellitus, a-synuclein associated with Parkinson’s disease, transthyretin V30M mutant associated with familial amyloid polyneuropathy, and Aβ42 associated with Alzheimer’s disease by stabilizing their respective protofibril intermediates. Kinetic studies employing the modeling software AmyloFit show that NUCB1 affects both primary nucleation and secondary nucleation. We hypothesize that NUCB1 binds to the common cross-β-sheet structure of protofibril aggregates to “cap” and stabilize soluble macromolecular complexes. Transmission electron microscopy and atomic force microscopy were employed to characterize the size, shape and volume distribution of multiple sources of NUCB1-capped protofibrils. Interestingly, NUCB1 prevents Aβ42 protofibril toxicity in a cellular assay. NUCB1-stabilized amyloid protofibrils could be used as immunogens to prepare conformation-specific antibodies and as novel tools to develop screens for anti-protofibril diagnostics and therapeutics. PMID:28220836

  23. Crystal Structure of Calmodulin Binding Domain of Orai1 in Complex with Ca2+•Calmodulin Displays a Unique Binding Mode*

    PubMed Central

    Liu, Yanshun; Zheng, Xunhai; Mueller, Geoffrey A.; Sobhany, Mack; DeRose, Eugene F.; Zhang, Yingpei; London, Robert E.; Birnbaumer, Lutz

    2012-01-01

    Orai1 is a plasma membrane protein that in its tetrameric form is responsible for calcium influx from the extracellular environment into the cytosol in response to interaction with the Ca2+-depletion sensor STIM1. This is followed by a fast Ca2+·calmodulin (CaM)-dependent inhibition, resulting from CaM binding to an Orai1 region called the calmodulin binding domain (CMBD). The interaction between Orai1 and CaM at the atomic level remains unknown. Here, we report the crystal structure of a CaM·Orai1-CMBD complex showing one CMBD bound to the C-terminal lobe of CaM, differing from other CaM-target protein complexes, in which both N- and C-terminal lobes of CaM (CaM-N and CaM-C) are involved in target binding. Orai1-CMBD binds CaM-C mainly through hydrophobic interactions, primarily involving residue Trp76 of Orai1-CMBD, which interacts with the hydrophobic pocket of CaM-C. However, NMR data, isothermal titration calorimetry data, and pulldown assays indicated that CaM-N and CaM-C both can bind Orai1-CMBD, with CaM-N having ∼4 times weaker affinity than CaM-C. Pulldown assays of a Orai1-CMBD(W76E) mutant, gel filtration chromatography data, and NOE signals indicated that CaM-N and CaM-C can each bind one Orai1-CMBD. Thus our studies support an unusual, extended 1:2 binding mode of CaM to Orai1-CMBDs, and quantify the affinity of Orai1 for CaM. We propose a two-step mechanism for CaM-dependent Orai1 inactivation initiated by binding of the C-lobe of CaM to the CMBD of one Orai1 followed by the binding of the N-lobe of CaM to the CMBD of a neighboring Orai1. PMID:23109337

  24. Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist

    NASA Astrophysics Data System (ADS)

    Cho, Nam-Chul; Seo, Seoung-Hwan; Kim, Dohee; Shin, Ji-Sun; Ju, Jeongmin; Seong, Jihye; Seo, Seon Hee; Lee, Iiyoun; Lee, Kyung-Tae; Kim, Yun Kyung; No, Kyoung Tai; Pae, Ae Nim

    2016-08-01

    Protease-activated receptor 2 (PAR2) is a G protein-coupled receptor, mediating inflammation and pain signaling in neurons, thus it is considered to be a potential therapeutic target for inflammatory diseases. In this study, we performed a ligand-based virtual screening of 1.6 million compounds by employing a common-feature pharmacophore model and two-dimensional similarity search to identify a new PAR2 antagonist. The common-feature pharmacophore model was established based on the biological screening results of our in-house library. The initial virtual screening yielded a total number of 47 hits, and additional biological activity tests including PAR2 antagonism and anti-inflammatory effects resulted in a promising candidate, compound 43, which demonstrated an IC50 value of 8.22 µM against PAR2. In next step, a PAR2 homology model was constructed using the crystal structure of the PAR1 as a template to explore the binding mode of the identified ligands. A molecular docking method was optimized by comparing the binding modes of a known PAR2 agonist GB110 and antagonist GB83, and applied to predict the binding mode of our hit compound 43. In-depth docking analyses revealed that the hydrophobic interaction with Phe2435.39 is crucial for PAR2 ligands to exert antagonistic activity. MD simulation results supported the predicted docking poses that PAR2 antagonist blocked a conformational rearrangement of Na+ allosteric site in contrast to PAR2 agonist that showed Na+ relocation upon GPCR activation. In conclusion, we identified new a PAR2 antagonist together with its binding mode, which provides useful insights for the design and development of PAR2 ligands.

  1. Discovery of a Potent Class of PI3Kα Inhibitors with Unique Binding Mode via Encoded Library Technology (ELT).

    PubMed

    Yang, Hongfang; Medeiros, Patricia F; Raha, Kaushik; Elkins, Patricia; Lind, Kenneth E; Lehr, Ruth; Adams, Nicholas D; Burgess, Joelle L; Schmidt, Stanley J; Knight, Steven D; Auger, Kurt R; Schaber, Michael D; Franklin, G Joseph; Ding, Yun; DeLorey, Jennifer L; Centrella, Paolo A; Mataruse, Sibongile; Skinner, Steven R; Clark, Matthew A; Cuozzo, John W; Evindar, Ghotas

    2015-05-14

    In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isoforms from a three-cycle DNA encoded library. An X-ray crystal structure of a representative inhibitor from this chemotype demonstrated a unique binding mode in the p110α protein.

  2. X-ray Crystallographic Studies Reveal That the Incorporation of Spacer Groups in Carbonic Anhydrase Inhibitors Causes Alternate Binding Modes

    SciTech Connect

    Fisher,S.; Govindasamy, L.; Boyle, N.; Agbandje-McKenna, M.; Silverman, D.; Blackburn, G.; McKenna, R.

    2006-01-01

    Human carbonic anhydrases (CAs) are well studied targets for the development of inhibitors for pharmaceutical applications. The crystal structure of human CA II has been determined in complex with two CA inhibitors (CAIs) containing conventional sulfonamide and thiadiazole moieties separated by a -CF{sub 2}- or -CHNH{sub 2}- spacer group. The structures presented here reveal that these spacer groups allow novel binding modes for the thiadiazole moiety compared with conventional CAIs.

  3. Structure, mechanics, and binding mode heterogeneity of LEDGF/p75-DNA nucleoprotein complexes revealed by scanning force microscopy

    NASA Astrophysics Data System (ADS)

    Vanderlinden, Willem; Lipfert, Jan; Demeulemeester, Jonas; Debyser, Zeger; de Feyter, Steven

    2014-04-01

    LEDGF/p75 is a transcriptional coactivator implicated in the pathogenesis of AIDS and leukemia. In these contexts, LEDGF/p75 acts as a cofactor by tethering protein cargo to transcriptionally active regions in the human genome. Our study - based on scanning force microscopy (SFM) imaging - is the first to provide structural information on the interaction of LEDGF/p75 with DNA. Two novel approaches that allow obtaining insights into the DNA conformation inside nucleoprotein complexes revealed (1) that LEDGF/p75 can bind at least in three different binding modes, (2) how DNA topology and protein dimerization affect these binding modes, and (3) geometrical and mechanical aspects of the nucleoprotein complexes. These structural and mechanical details will help us to better understand the cellular mechanisms of LEDGF/p75 as a transcriptional coactivator and as a cofactor in disease.LEDGF/p75 is a transcriptional coactivator implicated in the pathogenesis of AIDS and leukemia. In these contexts, LEDGF/p75 acts as a cofactor by tethering protein cargo to transcriptionally active regions in the human genome. Our study - based on scanning force microscopy (SFM) imaging - is the first to provide structural information on the interaction of LEDGF/p75 with DNA. Two novel approaches that allow obtaining insights into the DNA conformation inside nucleoprotein complexes revealed (1) that LEDGF/p75 can bind at least in three different binding modes, (2) how DNA topology and protein dimerization affect these binding modes, and (3) geometrical and mechanical aspects of the nucleoprotein complexes. These structural and mechanical details will help us to better understand the cellular mechanisms of LEDGF/p75 as a transcriptional coactivator and as a cofactor in disease. Electronic supplementary information (ESI) available: SFM topographs of phage lambda DNA in situ, in the absence and presence of LEDGF/p75; model-independent tests for DNA chain equilibration in 2D; SFM topographs of

  4. Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode.

    PubMed

    Cole, David K; Sami, Malkit; Scott, Daniel R; Rizkallah, Pierre J; Borbulevych, Oleg Y; Todorov, Penio T; Moysey, Ruth K; Jakobsen, Bent K; Boulter, Jonathan M; Baker, Brian M; Yi Li

    2013-01-01

    Natural T cell receptors (TCRs) generally bind to their cognate pMHC molecules with weak affinity and fast kinetics, limiting their use as therapeutic agents. Using phage display, we have engineered a high affinity version of the A6 wild-type TCR (A6wt), specific for the human leukocyte antigen (HLA-A(∗)0201) complexed with human T cell lymphotropic virus type 111-19 peptide (A2-Tax). Mutations in just 4 residues in the CDR3β loop region of the A6wt TCR were selected that improved binding to A2-Tax by nearly 1000-fold. Biophysical measurements of this mutant TCR (A6c134) demonstrated that the enhanced binding was derived through favorable enthalpy and a slower off-rate. The structure of the free A6c134 TCR and the A6c134/A2-Tax complex revealed a native binding mode, similar to the A6wt/A2-Tax complex. However, concordant with the more favorable binding enthalpy, the A6c134 TCR made increased contacts with the Tax peptide compared with the A6wt/A2-Tax complex, demonstrating a peptide-focused mechanism for the enhanced affinity that directly involved the mutated residues in the A6c134 TCR CDR3β loop. This peptide-focused enhanced TCR binding may represent an important approach for developing antigen specific high affinity TCR reagents for use in T cell based therapies.

  5. In-silico Investigation of Tubulin Binding Modes of a Series of Novel Antiproliferative Spiroisoxazoline Compounds Using Docking Studies

    PubMed Central

    Abolhasani, Hoda; Zarghi, Afshin; Hamzeh-Mivehroud, Maryam; Alizadeh, Ali Akbar; Shahbazi Mojarrad, Javid; Dastmalchi, Siavoush

    2015-01-01

    Interference with microtubule polymerization results in cell cycle arrest leading to cell death. Colchicine is a well-known microtubule polymerization inhibitor which does so by binding to a specific site on tubulin. A set of 3', 4'-bis (substituted phenyl)-4'H-spiro [indene-2, 5'-isoxazol]-1(3H)-one derivatives with known antiproliferative activities were evaluated for their tubulin binding modes. 3D structures of the derivatives were docked into the colchicine binding site of tubulin using GOLD 5.0 program under flexible ligand and semi-flexible receptor condition. The spiroisoxazoline derivatives bind tubulin in a similar manner to colchicine by establishing at least a hydrogen bonding to Cys241 as well as hydrophobic interactions with Leu255, Ile378 and Lys254 and few other residues at the binding pocket. It can be concluded that the spiroisoxazoline core structure common to the studied derivatives is a suitable scaffold for placing the antitubulin pharmacophoric groups in appropriate spatial positions required for tubulin binding activity. PMID:25561920

  6. ‘Carba’-carfentanil (trans isomer): a μ opioid receptor (MOR) partial agonist with a distinct binding mode

    PubMed Central

    Weltrowska, Grazyna; Lemieux, Carole; Chung, Nga N.; Guo, Jason J.; Wilkes, Brian C.; Schiller, Peter W.

    2014-01-01

    There is strong evidence to indicate that a positively charged nitrogen of endogenous and exogenous opioid ligands forms a salt bridge with the Asp residue in the third transmembrane helix of opioid receptors. To further examine the role of this electrostatic interaction in opioid receptor binding and activation, we synthesized ‘carba’-analogues of the highly potent μ opioid analgesic carfentanil (3), in which the piperidine nitrogen was replaced with a carbon. The resulting trans isomer (8b) showed reduced, but still significant MOR binding affinity (Kiμ = 95.2 nM) with no MOR versus DOR binding selectivity and was a MOR partial agonist. The cis isomer (8a) was essentially inactive. A MOR docking study indicated that 8b bound to the same binding pocket as parent 3, but its binding mode was somewhat different. A reevaluation of the uncharged morphine derivative N-formylnormorphine (9) indicated that it was a weak MOR antagonist showing no preference for MOR over KOR. Taken together, the results indicate that deletion of the positively charged nitrogen in μ opioid analgesics reduces MOR binding affinity by 2–3 orders of magnitude and may have pronounced effects on the intrinsic efficacy and on the opioid receptor selectivity profile. PMID:25129170

  7. A Study of the Predictive Relationships between Faculty Engagement, Learner Satisfaction and Outcomes in Multiple Learning Delivery Modes

    ERIC Educational Resources Information Center

    Yen, Cherng-Jyh; Abdous, M'hammed

    2012-01-01

    This study assessed the predictive relationships between faculty engagement, learner satisfaction, and outcomes across multiple learning delivery modes (LDMs). Participants were enrolled in courses with the options of three learning delivery modes: face-to-face, satellite broadcasting, and live video-streaming. The predictive relationship between…

  8. Multiple Ca2+ Binding Sites in the Extracellular Domain of Ca2+-Sensing Receptor Corresponding to Cooperative Ca2+ Response†

    PubMed Central

    Huang, Yun; Zhou, Yubin; Castiblanco, Adriana; Yang, Wei; Brown, Edward M.; Yang, Jenny J.

    2009-01-01

    A small change in the extracellular Ca2+ concentration ([Ca2+]o) integrates cell signaling responses in multiple cellular and tissue networks and functions via activation of Ca2+-sensing receptors (CaSR). Mainly through binding of Ca2+ to the large extracellular domain (ECD) of the dimeric CaSR, intracellular Ca2+ responses are highly cooperative with an apparent Hill coefficient ranging from 2 to 4. We have previously reported the identification of two continuous putative Ca2+-binding sites by grafting CaSR-derived, Ca2+-binding peptides to a scaffold protein, CD2, that does not bind Ca2+. In this paper, we predict more potential non-continuous Ca2+-binding sites in the ECD. We dissect the intact CaSR into three globular subdomains, each of which contains 2 to 3 predicted Ca2+-binding sites. This approach enables us to further understand the mechanisms underlying the binding of multiple metal ions to extended polypeptides derived from within the ECD of the CaSR, which would be anticipated to more closely mimic the structure of the native CaSR ECD. Tb3+-luminescence energy transfer, ANS fluorescence, and NMR studies show biphasic metal-binding components and Ca2+-dependent conformational changes in these subdomains. Removing the predicted Ca2+-binding ligands in site 1 and site 3 abolishes the first binding step and second binding step, respectively. Studies on these subdomains suggest the existence of multiple metal-binding sites and metal-induced conformational changes that might be responsible for switching on/off the CaSR by transition between its open inactive form and closed active form. PMID:19102677

  9. Deciphering the stepwise binding mode of HRG1β to HER3 by surface plasmon resonance and interaction map.

    PubMed

    Peess, Carmen; von Proff, Leopold; Goller, Sabine; Andersson, Karl; Gerg, Michael; Malmqvist, Magnus; Bossenmaier, Birgit; Schräml, Michael

    2015-01-01

    For the development of efficient anti-cancer therapeutics against the HER receptor family it is indispensable to understand the mechanistic model of the HER receptor activation upon ligand binding. Due to its high complexity the binding mode of Heregulin 1 beta (HRG1β) with its receptor HER3 is so far not understood. Analysis of the interaction of HRG1β with surface immobilized HER3 extracellular domain by time-resolved Surface Plasmon Resonance (SPR) was so far not interpretable using any regular analysis method as the interaction was highly complex. Here, we show that Interaction Map (IM) made it possible to shed light on this interaction. IM allowed deciphering the rate limiting kinetic contributions from complex SPR sensorgrams and thereby enabling the extraction of discrete kinetic rate components from the apparently heterogeneous interactions. We could resolve details from the complex avidity-driven binding mode of HRG1β with HER3 by using a combination of SPR and IM data. Our findings contribute to the general understanding that a major conformational change of HER3 during its activation is induced by a complex sequential HRG1β docking mode.

  10. Modeling of Beams’ Multiple-Contact Mode with an Application in the Design of a High-g Threshold Microaccelerometer

    PubMed Central

    Li, Kai; Chen, Wenyuan; Zhang, Weiping

    2011-01-01

    Beam’s multiple-contact mode, characterized by multiple and discrete contact regions, non-uniform stoppers’ heights, irregular contact sequence, seesaw-like effect, indirect interaction between different stoppers, and complex coupling relationship between loads and deformation is studied. A novel analysis method and a novel high speed calculation model are developed for multiple-contact mode under mechanical load and electrostatic load, without limitations on stopper height and distribution, providing the beam has stepped or curved shape. Accurate values of deflection, contact load, contact region and so on are obtained directly, with a subsequent validation by CoventorWare. A new concept design of high-g threshold microaccelerometer based on multiple-contact mode is presented, featuring multiple acceleration thresholds of one sensitive component and consequently small sensor size. PMID:22163897

  11. Dynamic control of polarization-inverted modes in three-dimensionally trapped multiple nanogaps

    SciTech Connect

    Tamura, Mamoru; Iida, Takuya

    2015-12-28

    We propose a guiding principle for the dynamic control of polarization-inverted modes in multiple nanogaps for unconventional optical transitions of molecules at arbitrary three-dimensional spatial positions. Based on our developed self-consistent theory for the optical assembly of nanoparticles (NPs), we clarified that spherical silver NPs can be optically trapped and aligned in the light-propagating direction via longitudinally polarized light; they form a rod-like nano-composite with multiple nanogaps. During trapping, there is a possibility that an additional irradiation of linearly polarized far-field light may excite the bonding and anti-bonding dark plasmon modes with low radiative decay rate of several meV via cancellation of inverted polarization. Our finding reveals that not only the steep change in the enhanced intensity of light field but also the phase inversion of light field between the dynamically formed nanogaps will pave the way to the highly sensitive sensors for molecules, the unconventional chemical reactions, and so on.

  12. End-to-End Rate-Distortion Optimized MD Mode Selection for Multiple Description Video Coding

    NASA Astrophysics Data System (ADS)

    Heng, Brian A.; Apostolopoulos, John G.; Lim, Jae S.

    2006-12-01

    Multiple description (MD) video coding can be used to reduce the detrimental effects caused by transmission over lossy packet networks. A number of approaches have been proposed for MD coding, where each provides a different tradeoff between compression efficiency and error resilience. How effectively each method achieves this tradeoff depends on the network conditions as well as on the characteristics of the video itself. This paper proposes an adaptive MD coding approach which adapts to these conditions through the use of adaptive MD mode selection. The encoder in this system is able to accurately estimate the expected end-to-end distortion, accounting for both compression and packet loss-induced distortions, as well as for the bursty nature of channel losses and the effective use of multiple transmission paths. With this model of the expected end-to-end distortion, the encoder selects between MD coding modes in a rate-distortion (R-D) optimized manner to most effectively tradeoff compression efficiency for error resilience. We show how this approach adapts to both the local characteristics of the video and network conditions and demonstrates the resulting gains in performance using an H.264-based adaptive MD video coder.

  13. Multiple GTP-binding proteins regulate vesicular transport from the ER to Golgi membranes

    PubMed Central

    1992-01-01

    Using indirect immunofluorescence we have examined the effects of reagents which inhibit the function of ras-related rab small GTP- binding proteins and heterotrimeric G alpha beta gamma proteins in ER to Golgi transport. Export from the ER was inhibited by an antibody towards rab1B and an NH2-terminal peptide which inhibits ARF function (Balch, W. E., R. A. Kahn, and R. Schwaninger. 1992. J. Biol. Chem. 267:13053-13061), suggesting that both of these small GTP-binding proteins are essential for the transport vesicle formation. Export from the ER was also potently inhibited by mastoparan, a peptide which mimics G protein binding regions of seven transmembrane spanning receptors activating and uncoupling heterotrimeric G proteins from their cognate receptors. Consistent with this result, purified beta gamma subunits inhibited the export of VSV-G from the ER suggesting an initial event in transport vesicle assembly was regulated by a heterotrimeric G protein. In contrast, incubation in the presence of GTP gamma S or AIF(3-5) resulted in the accumulation of transported protein in different populations of punctate pre-Golgi intermediates distributed throughout the cytoplasm of the cell. Finally, a peptide which is believed to antagonize the interaction of rab proteins with putative downstream effector molecules inhibited transport at a later step preceding delivery to the cis Golgi compartment, similar to the site of accumulation of transported protein in the absence of NSF or calcium (Plutner, H., H. W. Davidson, J. Saraste, and W. E. Balch. 1992. J. Cell Biol. 119:1097-1116). These results are consistent with the hypothesis that multiple GTP-binding proteins including a heterotrimeric G protein(s), ARF and rab1 differentially regulate steps in the transport of protein between early compartments of the secretory pathway. The concept that G protein-coupled receptors gate the export of protein from the ER is discussed. PMID:1447289

  14. Determination of the cationic amphiphilic drug-DNA binding mode and DNA-assisted fluorescence resonance energy transfer amplification

    NASA Astrophysics Data System (ADS)

    Yaseen, Zahid; Banday, Abdul Rouf; Hussain, Mohammed Aamir; Tabish, Mohammad; Kabir-ud-Din

    2014-03-01

    Understanding the mechanism of drug-DNA binding is crucial for predicting the potential genotoxicity of drugs. Agarose gel electrophoresis, absorption, steady state fluorescence, and circular dichroism have been used in exploring the interaction of cationic amphiphilic drugs (CADs) such as amitriptyline hydrochloride (AMT), imipramine hydrochloride (IMP), and promethazine hydrochloride (PMT) with calf thymus or pUC19 DNA. Agarose gel electrophoresis assay, along with absorption and steady state fluorescence studies, reveal interaction between the CADs and DNA. A comparative study of the drugs with respect to the effect of urea, iodide induced quenching, and ethidium bromide (EB) exclusion assay reflects binding of CADs to the DNA primarily in an intercalative fashion. Circular dichroism data also support the intercalative mode of binding. Besides quenching, there is fluorescence exchange energy transfer (FRET) in between CADs and EB using DNA as a template.

  15. Multiple-mode nonlinear free and forced vibrations of beams using finite element method

    NASA Technical Reports Server (NTRS)

    Mei, Chuh; Decha-Umphai, Kamolphan

    1987-01-01

    Multiple-mode nonlinear free and forced vibration of a beam is analyzed by the finite element method. The geometric nonlinearity is investigated. Inplane displacement and inertia (IDI) are also considered in the formulation. Harmonic force matrix is derived and explained. Nonlinear free vibration can be simply treated as a special case of the general forced vibration by setting the harmonic force matrix equal to zero. The effect of the higher modes is more pronouced for the clamped supported beam than the simply supported one. Beams without IDI yield more effect of the higher modes than the one with IDI. The effects of IDI are to reduce nonlinearity. For beams with end supports restrained from axial movement (immovable cases), only the hardening type nonlinearity is observed. However, beams of small slenderness ratio (L/R = 20) with movable end supports, the softening type nonlinearity is found. The concentrated force case yields a more severe response than the uniformly distributed force case. Finite element results are in good agreement with the solution of simple elliptic response, harmonic balance method, and Runge-Kutte method and experiment.

  16. Further Insights in the Binding Mode of Selective Inhibitors to Human PDE4D Enzyme Combining Docking and Molecular Dynamics

    PubMed Central

    D'Ursi, Pasqualina; Guariento, Sara; Trombetti, Gabriele; Orro, Alessandro; Cichero, Elena; Milanesi, Luciano; Bruno, Olga

    2016-01-01

    Abstract Alzheimer′s disease has recently emerged as a possible field of application for PDE4D inhibitors (PDE4DIs). The great structure similarity among the various PDE4 isoforms and, furthermore, the lack of the full length crystal structure of the enzyme, impaired the rational design of new selective PDE4DIs. In this paper, with the aim of exploring new insights into the PDE4D binding, we tackled the problem by performing a computational study based on docking simulations combined with molecular dynamics (D‐MD). Our work uniquely identified the binding mode and the key residues involved in the interaction with a number of in‐house catechol iminoether derivatives, acting as PDE4DIs. Moreover, the new binding mode was tested using a series of analogues previously reported by us and it was used to confirm their key structural features to allow PDE4D inhibition. The binding model disclosed within the current computational study may prove to be useful to further advance the design and synthesis of novel, more potent and selective, PDE4D inhibitors. PMID:27546041

  17. Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase

    PubMed Central

    2016-01-01

    Oxalate decarboxylase (OxDC) catalyzes the conversion of oxalate into formate and carbon dioxide in a remarkable reaction that requires manganese and dioxygen. Previous studies have shown that replacing an active-site loop segment Ser161-Glu162-Asn163-Ser164 in the N-terminal domain of OxDC with the cognate residues Asp161-Ala162-Ser-163-Asn164 of an evolutionarily related, Mn-dependent oxalate oxidase gives a chimeric variant (DASN) that exhibits significantly increased oxidase activity. The mechanistic basis for this change in activity has now been investigated using membrane inlet mass spectrometry (MIMS) and isotope effect (IE) measurements. Quantitative analysis of the reaction stoichiometry as a function of oxalate concentration, as determined by MIMS, suggests that the increased oxidase activity of the DASN OxDC variant is associated with only a small fraction of the enzyme molecules in solution. In addition, IE measurements show that C–C bond cleavage in the DASN OxDC variant proceeds via the same mechanism as in the wild-type enzyme, even though the Glu162 side chain is absent. Thus, replacement of the loop residues does not modulate the chemistry of the enzyme-bound Mn(II) ion. Taken together, these results raise the possibility that the observed oxidase activity of the DASN OxDC variant arises from an increased level of access of the solvent to the active site during catalysis, implying that the functional role of Glu162 is to control loop conformation. A 2.6 Å resolution X-ray crystal structure of a complex between oxalate and the Co(II)-substituted ΔE162 OxDC variant, in which Glu162 has been deleted from the active site loop, reveals the likely mode by which the substrate coordinates the catalytically active Mn ion prior to C–C bond cleavage. The “end-on” conformation of oxalate observed in the structure is consistent with the previously published V/K IE data and provides an empty coordination site for the dioxygen ligand that is thought to

  18. Selective JAK3 Inhibitors with a Covalent Reversible Binding Mode Targeting a New Induced Fit Binding Pocket.

    PubMed

    Forster, Michael; Chaikuad, Apirat; Bauer, Silke M; Holstein, Julia; Robers, Matthew B; Corona, Cesear R; Gehringer, Matthias; Pfaffenrot, Ellen; Ghoreschi, Kamran; Knapp, Stefan; Laufer, Stefan A

    2016-11-17

    Janus kinases (JAKs) are a family of cytoplasmatic tyrosine kinases that are attractive targets for the development of anti-inflammatory drugs given their roles in cytokine signaling. One question regarding JAKs and their inhibitors that remains under intensive debate is whether JAK inhibitors should be isoform selective. Since JAK3 functions are restricted to immune cells, an isoform-selective inhibitor for JAK3 could be especially valuable to achieve clinically more useful and precise effects. However, the high degree of structural conservation makes isoform-selective targeting a challenging task. Here, we present picomolar inhibitors with unprecedented kinome-wide selectivity for JAK3. Selectivity was achieved by concurrent covalent reversible targeting of a JAK3-specific cysteine residue and a ligand-induced binding pocket. We confirmed that in vitro activity and selectivity translate well into the cellular environment and suggest that our inhibitors are powerful tools to elucidate JAK3-specific functions.

  19. Alpha-Amylase Starch Binding Domains: Cooperative Effects of Binding to Starch Granules of Multiple Tandemly Arranged Domains▿

    PubMed Central

    Guillén, D.; Santiago, M.; Linares, L.; Pérez, R.; Morlon, J.; Ruiz, B.; Sánchez, S.; Rodríguez-Sanoja, R.

    2007-01-01

    The Lactobacillus amylovorus alpha-amylase starch binding domain (SBD) is a functional domain responsible for binding to insoluble starch. Structurally, this domain is dissimilar from other reported SBDs because it is composed of five identical tandem modules of 91 amino acids each. To understand adsorption phenomena specific to this SBD, the importance of their modular arrangement in relationship to binding ability was investigated. Peptides corresponding to one, two, three, four, or five modules were expressed as His-tagged proteins. Protein binding assays showed an increased capacity of adsorption as a function of the number of modules, suggesting that each unit of the SBD may act in an additive or synergic way to optimize binding to raw starch. PMID:17468268

  20. Alpha-amylase starch binding domains: cooperative effects of binding to starch granules of multiple tandemly arranged domains.

    PubMed

    Guillén, D; Santiago, M; Linares, L; Pérez, R; Morlon, J; Ruiz, B; Sánchez, S; Rodríguez-Sanoja, R

    2007-06-01

    The Lactobacillus amylovorus alpha-amylase starch binding domain (SBD) is a functional domain responsible for binding to insoluble starch. Structurally, this domain is dissimilar from other reported SBDs because it is composed of five identical tandem modules of 91 amino acids each. To understand adsorption phenomena specific to this SBD, the importance of their modular arrangement in relationship to binding ability was investigated. Peptides corresponding to one, two, three, four, or five modules were expressed as His-tagged proteins. Protein binding assays showed an increased capacity of adsorption as a function of the number of modules, suggesting that each unit of the SBD may act in an additive or synergic way to optimize binding to raw starch.

  1. Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor

    PubMed Central

    Kim, Minsik; Kim, Hee Jung; Son, Sang Hyeon; Yoon, Hye Jin; Lim, Youngbin; Lee, Jong Woo; Seok, Yeong-Jae; Jin, Kyeong Sik; Yu, Yeon Gyu; Kim, Seong Keun; Ryu, Sangryeol; Lee, Hyung Ho

    2016-01-01

    DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92–198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant. PMID:27099293

  2. Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)

    PubMed Central

    Kim, Doyoun; Hur, Jeonghwan; Park, Kwangsoo; Bae, Sangsu; Shin, Donghyuk; Ha, Sung Chul; Hwang, Hye-Yeon; Hohng, Sungchul; Lee, Joon-Hwa; Lee, Sangho; Kim, Yang-Gyun; Kim, Kyeong Kyu

    2014-01-01

    Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains, performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response, we performed structural and functional studies of the Z-DNA binding domain (Zα) of PKZ from Carassius auratus (caZαPKZ). The 1.7-Å resolution crystal structure of caZαPKZ:Z-DNA revealed that caZαPKZ shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZαPKZ and its mutants revealed that caZαPKZ mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZαPKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the β-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZαPKZ further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these results together, we conclude that the positive charge in the β-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate. PMID:24682817

  3. Mean deviation coupling synchronous control for multiple motors via second-order adaptive sliding mode control.

    PubMed

    Li, Lebao; Sun, Lingling; Zhang, Shengzhou

    2016-05-01

    A new mean deviation coupling synchronization control strategy is developed for multiple motor control systems, which can guarantee the synchronization performance of multiple motor control systems and reduce complexity of the control structure with the increasing number of motors. The mean deviation coupling synchronization control architecture combining second-order adaptive sliding mode control (SOASMC) approach is proposed, which can improve synchronization control precision of multiple motor control systems and make speed tracking errors, mean speed errors of each motor and speed synchronization errors converge to zero rapidly. The proposed control scheme is robustness to parameter variations and random external disturbances and can alleviate the chattering phenomena. Moreover, an adaptive law is employed to estimate the unknown bound of uncertainty, which is obtained in the sense of Lyapunov stability theorem to minimize the control effort. Performance comparisons with master-slave control, relative coupling control, ring coupling control, conventional PI control and SMC are investigated on a four-motor synchronization control system. Extensive comparative results are given to shown the good performance of the proposed control scheme.

  4. Characterization of nicotine binding to the rat brain P/sub 2/ preparation: the identification of multiple binding sites which include specific up-regulatory site(s)

    SciTech Connect

    Sloan, J.W.

    1984-01-01

    These studies show that nicotine binds to the rat brain P/sub 2/ preparation by saturable and reversible processes. Multiple binding sites were revealed by the configuration of saturation, kinetic and Scatchard plots. A least squares best fit of Scatchard data using nonlinear curve fitting programs confirmed the presence of a very high affinity site, an up-regulatory site, a high affinity site and one or two low affinity sites. Stereospecificity was demonstrated for the up-regulatory site where (+)-nicotine was more effective and for the high affinity site where (-)-nicotine had a higher affinity. Drugs which selectively up-regulate nicotine binding site(s) have been identified. Further, separate very high and high affinity sites were identified for (-)- and (+)-(/sup 3/H)nicotine, based on evidence that the site density for the (-)-isomer is 10 times greater than that for the (+)-isomer at these sites. Enhanced nicotine binding has been shown to be a statistically significant phenomenon which appears to be a consequence of drugs binding to specific site(s) which up-regulate binding at other site(s). Although Scatchard and Hill plots indicate positive cooperatively, up-regulation more adequately describes the function of these site(s). A separate up-regulatory site is suggested by the following: (1) Drugs vary markedly in their ability to up-regulate binding. (2) Both the affinity and the degree of up-regulation can be altered by structural changes in ligands. (3) Drugs with specificity for up-regulation have been identified. (4) Some drugs enhance binding in a dose-related manner. (5) Competition studies employing cold (-)- and (+)-nicotine against (-)- and (+)-(/sup 3/H)nicotine show that the isomers bind to separate sites which up-regulate binding at the (-)- and (+)-nicotine high affinity sites and in this regard (+)-nicotine is more specific and efficacious than (-)-nicotine.

  5. Component mode synthesis and large deflection vibration of complex structures. Volume 3: Multiple-mode nonlinear free and forced vibrations of beams using finite element method

    NASA Technical Reports Server (NTRS)

    Mei, Chuh; Shen, Mo-How

    1987-01-01

    Multiple-mode nonlinear forced vibration of a beam was analyzed by the finite element method. Inplane (longitudinal) displacement and inertia (IDI) are considered in the formulation. By combining the finite element method and nonlinear theory, more realistic models of structural response are obtained more easily and faster.

  6. Fabric Controls on the Failure Mode of Strongly Deformed Metamorphic Rocks with Multiple Anisotropies

    NASA Astrophysics Data System (ADS)

    Agliardi, F.; Zanchetta, S.; Crosta, G. B.; Barberini, V.; Fusi, N.; De Ponti, E.

    2012-12-01

    resolutions (MicroCT: 40-60 μm; medical CT: 625 μm) and micro-structural analysis of thin sections. Investigation results suggest that the failure of strongly deformed metamorphic rocks is controlled by the occurrence of multiple anisotropies related to micro-fabric, not always characterised by clear meso-scale expression, including crenulation folding, shape preferred orientation, intracrystalline deformation microstructure. Different failure modes dominate depending on the geometrical arrangement of both foliation and fold axial surfaces, in turn affecting the values of rock strength and deformability. The results of this study point to the need of accounting for the effects of multiple, geometrically complex anisotropies in setting up realistic models of rock fracturing at different scale and for different geological and engineering applications.

  7. Multiple Evolutionary Origins of Ubiquitous Cu2+ and Zn2+ Binding in the S100 Protein Family

    PubMed Central

    Wheeler, Lucas C.; Donor, Micah T.; Prell, James S.

    2016-01-01

    The S100 proteins are a large family of signaling proteins that play critical roles in biology and disease. Many S100 proteins bind Zn2+, Cu2+, and/or Mn2+ as part of their biological functions; however, the evolutionary origins of binding remain obscure. One key question is whether divalent transition metal binding is ancestral, or instead arose independently on multiple lineages. To tackle this question, we combined phylogenetics with biophysical characterization of modern S100 proteins. We demonstrate an earlier origin for established S100 subfamilies than previously believed, and reveal that transition metal binding is widely distributed across the tree. Using isothermal titration calorimetry, we found that Cu2+ and Zn2+ binding are common features of the family: the full breadth of human S100 paralogs—as well as two early-branching S100 proteins found in the tunicate Oikopleura dioica—bind these metals with μM affinity and stoichiometries ranging from 1:1 to 3:1 (metal:protein). While binding is consistent across the tree, structural responses to binding are quite variable. Further, mutational analysis and structural modeling revealed that transition metal binding occurs at different sites in different S100 proteins. This is consistent with multiple origins of transition metal binding over the evolution of this protein family. Our work reveals an evolutionary pattern in which the overall phenotype of binding is a constant feature of S100 proteins, even while the site and mechanism of binding is evolutionarily labile. PMID:27764152

  8. The binding mode of human nucleoside diphosphate kinase B to single-strand DNA.

    PubMed

    Agou, F; Raveh, S; Véron, M

    2000-06-01

    In this paper, we studied the interaction of the human isoform B of nucleoside diphosphate kinase (NDP kinase B) with the nuclease hypersensitive element (NHE) present in the promoter element of the c-myc oncogene. The DNA-binding properties of NDP kinase B and other NDP kinases are compared and the nucleotide requirement for binding are discussed. Using quantitative methods, we identified the DNA-binding sites on the protein and we proposed a structural model for a complex of one hexameric NDP kinase B with an oligonucleotide.

  9. Synergistic effects of multiple treatments, and both DNA and RNA direct bindings on, green tea catechins.

    PubMed

    Kuzuhara, Takashi; Tanabe, Akitoshi; Sei, Yoshihisa; Yamaguchi, Kentaro; Suganuma, Masami; Fujiki, Hirota

    2007-08-01

    This article reviews two main topics: (1) the synergistic effects of multiple treatments with green tea catechin and (2) the direct binding of (-)-epigallocatechin gallate (EGCG) to both DNA and RNA molecules. Japanese drink green tea throughout the day, so we studied whether multiple treatments of cells with EGCG would enhance the expression of apoptosis-related genes, such as growth arrest and DNA damage-inducible gene (GADD153) and cyclin-dependent kinase inhibitor gene (p21(waf1)): The results suggest that the synergistic enhancement of both GADD153 and p21(waf1) gene expressions by multiple treatments plays a significant role in human cancer prevention with green tea beverage. Our previous observation-that nucleic acids extracted from catechin-treated cells are colored-allowed us to speculate that catechins directly interact with nucleic acids. Surface plasmon resonance assay (Biacore) indicated that four catechins, EGCG, (-)-epicatechin gallate (ECG), (+)-gallocatechin gallate (GCG), and (+)-catechin gallate (CG), bound to DNA oligomers. Cold spray ionization mass spectrometry (CSI-MS) analysis showed that one to three EGCG molecules bound to single-stranded 18 mers of DNA and RNA. Moreover, one or two molecules of EGCG bound to double-stranded AG:CT oligomers of various nucleotide lengths. Double-stranded DNA (dsDNA) oligomers were detected only as EGCG-bound forms at high temperature, whereas at low temperature both the free and bound forms were detected, suggesting that EGCG protects double-stranded DNA oligomers from double-stranded melting into single-stranded DNA. We assume that catechins accumulate in both double-stranded DNA and RNA molecules through multiple administrations of green tea beverage in in vivo, and that the accumulated green tea catechins play a significant role for human cancer prevention.

  10. Multiple Plasmodium falciparum Merozoite Surface Protein 1 Complexes Mediate Merozoite Binding to Human Erythrocytes.

    PubMed

    Lin, Clara S; Uboldi, Alessandro D; Epp, Christian; Bujard, Hermann; Tsuboi, Takafumi; Czabotar, Peter E; Cowman, Alan F

    2016-04-01

    Successful invasion of human erythrocytes byPlasmodium falciparummerozoites is required for infection of the host and parasite survival. The early stages of invasion are mediated via merozoite surface proteins that interact with human erythrocytes. The nature of these interactions are currently not well understood, but it is known that merozoite surface protein 1 (MSP1) is critical for successful erythrocyte invasion. Here we show that the peripheral merozoite surface proteins MSP3, MSP6, MSPDBL1, MSPDBL2, and MSP7 bind directly to MSP1, but independently of each other, to form multiple forms of the MSP1 complex on the parasite surface. These complexes have overlapping functions that interact directly with human erythrocytes. We also show that targeting the p83 fragment of MSP1 using inhibitory antibodies inhibits all forms of MSP1 complexes and disrupts parasite growthin vitro.

  11. Hedgehog Pathway Modulation by Multiple Lipid Binding Sites on the Smoothened Effector of Signal Response

    PubMed Central

    Myers, Benjamin R.; Sever, Navdar; Chong, Yong Chun; Kim, James; Belani, Jitendra D.; Rychnovsky, Scott; Bazan, J. Fernando; Beachy, Philip A.

    2014-01-01

    Summary Hedgehog (Hh) signaling during development and in postembryonic tissues requires activation of the 7TM oncoprotein Smoothened (Smo), by mechanisms that may involve endogenous lipidic modulators. Exogenous Smo ligands previously identified include the plant sterol cyclopamine (and its therapeutically useful synthetic mimics) and hydroxylated cholesterol derivatives (oxysterols); Smo is also highly sensitive to cellular sterol levels. The relationships between these effects are unclear because the relevant Smo structural determinants are unknown. We identify the conserved extracellular cysteine rich domain (CRD) as the site of action for oxysterols on Smo, involving residues structurally analogous to those contacting the Wnt lipid adduct in the homologous Frizzled CRD; this modulatory effect is distinct from that of cyclopamine mimics, from Hh-mediated regulation, and from the permissive action of cellular sterol pools. These results imply that Hh pathway activity is sensitive to lipid binding at several Smo sites, suggesting mechanisms for tuning by multiple physiological inputs. PMID:23954590

  12. MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

    SciTech Connect

    Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN.; Eisen, Michael B.

    2004-10-28

    We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

  13. Multiple ion binding sites in Ih channels of rod photoreceptors from tiger salamanders.

    PubMed

    Wollmuth, L P

    1995-05-01

    The mechanism of ion permeation in K+/Na(+)-permeable Ih channels of tiger salamander rod photoreceptors was investigated using the whole-cell voltage-clamp technique. Ih channels showed features indicative of pores with multiple ion binding sites: in mixtures of K+ and thallium (T1+), the amplitude of the time-dependent current showed an anomalous mole fraction dependence, and K+ permeation was blocked by other permeant ions (with K0.5 values: T1+, 44 microM; Rb+, 220 microM and NH4+, 1100 microM) as well as by essentially impermeant ions (Cs+, 22 microM Ba2+, 9200 microM) which apparently block Ih by binding in the pore. In contrast, Na+ had little blocking action on K+ permeation. The block by all of these ions was sensitive to external K+ with the block by Cs+ being the least sensitive. Na+ was more effective than K+ in reducing the block by T1+, Rb+ and NH4+, but was less effective for the block by Cs+ and Ba2+. The blocking action of Cs+ and Ba2+ was non-competitive, suggesting that they block Ih channels at independent sites. Based on the efficacy of block by the different ions, the degree to which K+ and Na+ antagonize this block and the noncompetitive blocking action of Cs+ and Ba2+, the permeation pathway of Ih channels appears to contain at least three ion binding sites with at least two sites having a higher affinity for K+ over Na+ and another site with a higher affinity for Na+ over K+.

  14. Transient Protein-Protein Interaction of the SH3-Peptide Complex via Closely Located Multiple Binding Sites

    PubMed Central

    Hahn, Seungsoo; Kim, Dongsup

    2012-01-01

    Protein-protein interactions play an essential role in cellular processes. Certain proteins form stable complexes with their partner proteins, whereas others function by forming transient complexes. The conventional protein-protein interaction model describes an interaction between two proteins under the assumption that a protein binds to its partner protein through a single binding site. In this study, we improved the conventional interaction model by developing a Multiple-Site (MS) model in which a protein binds to its partner protein through closely located multiple binding sites on a surface of the partner protein by transiently docking at each binding site with individual binding free energies. To test this model, we used the protein-protein interaction mediated by Src homology 3 (SH3) domains. SH3 domains recognize their partners via a weak, transient interaction and are therefore promiscuous in nature. Because the MS model requires large amounts of data compared with the conventional interaction model, we used experimental data from the positionally addressable syntheses of peptides on cellulose membranes (SPOT-synthesis) technique. From the analysis of the experimental data, individual binding free energies for each binding site of peptides were extracted. A comparison of the individual binding free energies from the analysis with those from atomistic force fields gave a correlation coefficient of 0.66. Furthermore, application of the MS model to 10 SH3 domains lowers the prediction error by up to 9% compared with the conventional interaction model. This improvement in prediction originates from a more realistic description of complex formation than the conventional interaction model. The results suggested that, in many cases, SH3 domains increased the protein complex population through multiple binding sites of their partner proteins. Our study indicates that the consideration of general complex formation is important for the accurate description of

  15. Properties of natural and artificial proteins displaying multiple ubiquitin-binding domains.

    PubMed

    Lopitz-Otsoa, Fernando; Rodríguez, Manuel S; Aillet, Fabienne

    2010-02-01

    Ubiquitylation provides a rapid alternative to control the activity of crucial cellular factors through the remodelling of a target protein. Diverse ubiquitin chains are recognized by domains with affinity for UBDs (ubiquitin-binding domains) present in receptor/effector proteins. Interestingly, some proteins contain more than one UBD and the preservation of this structure in many species suggests an evolutionary advantage for this topology. Here, we review some typical proteins that naturally contain more than one UBD and emphasize how such structures contribute to the mechanism they mediate. Characteristics such as higher affinities for polyubiquitin chains and chain-linkage preferences can be replicated by the TUBEs (tandem ubiquitin-binding entities). Furthermore, TUBEs show two additional properties: protection of ubiquitylated substrates from deubiquitylating enzymes and interference with the action of the proteasome. Consequently, TUBEs behave as 'ubiquitin traps' that efficiently capture endogenous ubiquitylated proteins. Interpretations and hypothetical models proposed by different groups to understand the synchronous action of multiple UBDs are discussed herein.

  16. Protein binding of isofluorophate in vivo after coexposure to multiple chemicals.

    PubMed Central

    Vogel, John S; Keating, Garrett A; Buchholz, Bruce A

    2002-01-01

    Full toxicologic profiles of chemical mixtures, including dose-response extrapolations to realistic exposures, is a prohibitive analytical problem, even for a restricted class of chemicals. We present an approach to probing in vivo interactions of pesticide mixtures at relevant low doses using a monitor compound to report the response of biochemical pathways shared by mixture components. We use accelerator mass spectrometry (AMS) to quantify [14C]-diisopropylfluorophosphate as a tracer at attomole levels with 1-5% precision after coexposures to parathion (PTN), permethrin (PER), and pyridostigmine bromide separately and in conjunction. Pyridostigmine shows an overall protective effect against tracer binding in plasma, red blood cells, muscle, and brain that is not explained as competitive protein binding. PTN and PER induce a significant 25-30% increase in the amount of tracer reaching the brain with or without pyridostigmine. The sensitivity of AMS for isotope-labeled tracer compounds can be used to probe the physiologic responses of specific biochemical pathways to multiple compound exposures. PMID:12634135

  17. Multiple DNA binding activities of the novel site-specific recombinase, Piv, from Moraxella lacunata.

    PubMed

    Tobiason, D M; Lenich, A G; Glasgow, A C

    1999-04-02

    The recombinase, Piv, is essential for site-specific DNA inversion of the type IV pilin DNA segment in Moraxella lacunata and Moraxella bovis. Piv shows significant homology with the transposases of the IS110/IS492 family of insertion elements, but, surprisingly, Piv contains none of the conserved amino acid motifs of the lambda Int or Hin/Res families of site-specific recombinases. Therefore, Piv may mediate site-specific recombination by a novel mechanism. To begin to determine how Piv may assemble a synaptic nucleoprotein structure for DNA cleavage and strand exchange, we have characterized the interaction of Piv with the DNA inversion region of M. lacunata. Gel shift and nuclease/chemical protection assays, competition and dissociation rate analyses, and cooperativity studies indicate that Piv binds two distinct recognition sequences. One recognition sequence, found at multiple sites within and outside of the invertible segment, is bound by Piv protomers with high affinity. The second recognition sequence is located at the recombination cross-over sites at the ends of the invertible element; Piv interacts with this sequence as an oligomer with apparent low affinity. A model is proposed for the role of the different Piv binding sites of the M. lacunata inversion region in the formation of an active synaptosome.

  18. A Compendium of Caenorhabditis elegans RNA Binding Proteins Predicts Extensive Regulation at Multiple Levels

    PubMed Central

    Tamburino, Alex M.; Ryder, Sean P.; Walhout, Albertha J. M.

    2013-01-01

    Gene expression is regulated at multiple levels, including transcription and translation, as well as mRNA and protein stability. Although systems-level functions of transcription factors and microRNAs are rapidly being characterized, few studies have focused on the posttranscriptional gene regulation by RNA binding proteins (RBPs). RBPs are important to many aspects of gene regulation. Thus, it is essential to know which genes encode RBPs, which RBPs regulate which gene(s), and how RBP genes are themselves regulated. Here we provide a comprehensive compendium of RBPs from the nematode Caenorhabditis elegans (wRBP1.0). We predict that as many as 887 (4.4%) of C. elegans genes may encode RBPs ~250 of which likely function in a gene-specific manner. In addition, we find that RBPs, and most notably gene-specific RBPs, are themselves enriched for binding and modification by regulatory proteins, indicating the potential for extensive regulation of RBPs at many different levels. wRBP1.0 will provide a significant contribution toward the comprehensive delineation of posttranscriptional regulatory networks and will provide a resource for further studies regulation by RBPs. PMID:23390605

  19. Structural Studies of an Engineered Zinc Biosensor Reveal an Unanticipated Mode of Zinc Binding

    SciTech Connect

    Telmer,P.; Shilton, B.

    2005-01-01

    Protein engineering was used previously to convert maltose-binding protein (MBP) into a zinc biosensor. Zn{sup 2+} binding by the engineered MBP was thought to require a large conformational change from 'open' to 'closed', similar to that observed when maltose is bound by the wild-type protein. We show that although this re-designed MBP molecule binds Zn{sup 2+} with high affinity as previously reported, it does not adopt a closed conformation in solution as assessed by small-angle X-ray scattering. High-resolution crystallographic studies of the engineered Zn{sup 2+}-binding MBP molecule demonstrate that Zn{sup 2+} is coordinated by residues on the N-terminal lobe only, and therefore Zn{sup 2+} binding does not require the protein to adopt a fully closed conformation. Additional crystallographic studies indicate that this unexpected Zn{sup 2+} binding site can also coordinate Cu{sup 2+} and Ni{sup 2+} with only subtle changes in the overall conformation of the protein. This work illustrates that the energetic barrier to domain closure, which normally functions to maintain MBP in an open concentration in the absence of ligand, is not easily overcome by protein design. A comparison to the mechanism of maltose-induced domain rearrangement is discussed.

  20. Universal limiting shape of worn profile under multiple-mode fretting conditions: theory and experimental evidence

    NASA Astrophysics Data System (ADS)

    Dmitriev, Andrey I.; Voll, Lars B.; Psakhie, Sergey G.; Popov, Valentin L.

    2016-03-01

    We consider multiple-mode fretting wear in a frictional contact of elastic bodies subjected to a small-amplitude oscillation, which may include in-plane and out-of-plane translation, torsion and tilting (“periodic rolling”). While the detailed kinetics of wear depends on the particular loading history and wear mechanism, the final worn shape, under some additional conditions, occurs to be universal for all types and loading and wear mechanisms. This universal form is determined solely by the radius of the permanent stick region and the maximum indentation depth during the loading cycle. We provide experimental evidence for the correctness of the theoretically predicted limiting shape. The existence of the universal limiting shape can be used for designing joints which are resistant to fretting wear.

  1. Universal limiting shape of worn profile under multiple-mode fretting conditions: theory and experimental evidence

    PubMed Central

    Dmitriev, Andrey I.; Voll, Lars B.; Psakhie, Sergey G.; Popov, Valentin L.

    2016-01-01

    We consider multiple-mode fretting wear in a frictional contact of elastic bodies subjected to a small-amplitude oscillation, which may include in-plane and out-of-plane translation, torsion and tilting (“periodic rolling”). While the detailed kinetics of wear depends on the particular loading history and wear mechanism, the final worn shape, under some additional conditions, occurs to be universal for all types and loading and wear mechanisms. This universal form is determined solely by the radius of the permanent stick region and the maximum indentation depth during the loading cycle. We provide experimental evidence for the correctness of the theoretically predicted limiting shape. The existence of the universal limiting shape can be used for designing joints which are resistant to fretting wear. PMID:26979092

  2. Using input command pre-shaping to suppress multiple mode vibration

    NASA Technical Reports Server (NTRS)

    Hyde, James M.; Seering, Warren P.

    1990-01-01

    Spacecraft, space-borne robotic systems, and manufacturing equipment often utilize lightweight materials and configurations that give rise to vibration problems. Prior research has led to the development of input command pre-shapers that can significantly reduce residual vibration. These shapers exhibit marked insensitivity to errors in natural frequency estimates and can be combined to minimize vibration at more than one frequency. This paper presents a method for the development of multiple mode input shapers which are simpler to implement than previous designs and produce smaller system response delays. The new technique involves the solution of a group of simultaneous non-linear impulse constraint equations. The resulting shapers were tested on a model of MACE, an MIT/NASA experimental flexible structure.

  3. Heralded generation of single photons entangled in multiple temporal modes with controllable waveforms

    NASA Astrophysics Data System (ADS)

    Gogyan, A.; Sisakyan, N.; Akhmedzhanov, R.; Malakyan, Yu

    2014-11-01

    Time-bin entangled single-photons are highly demanded for long distance quantum communication. We propose a heralded source of tunable narrowband single photons entangled in well-separated multiple temporal modes (time bins) with controllable amplitudes. The detection of a single Stokes photon generated in a cold atomic ensemble via Raman scattering of a weak write pulse heralds the preparation of one spin excitation stored within the atomic medium. A train of read laser pulses deterministically converts the atomic excitation into a single anti-Stokes photon delocalized in multi-time-bins. The waveforms of bins are well-controlled by the read pulse parameters. A scheme to measure the phase coherence across all time bins is suggested.

  4. Speed tracking and synchronization of multiple motors using ring coupling control and adaptive sliding mode control.

    PubMed

    Li, Le-Bao; Sun, Ling-Ling; Zhang, Sheng-Zhou; Yang, Qing-Quan

    2015-09-01

    A new control approach for speed tracking and synchronization of multiple motors is developed, by incorporating an adaptive sliding mode control (ASMC) technique into a ring coupling synchronization control structure. This control approach can stabilize speed tracking of each motor and synchronize its motion with other motors' motion so that speed tracking errors and synchronization errors converge to zero. Moreover, an adaptive law is exploited to estimate the unknown bound of uncertainty, which is obtained in the sense of Lyapunov stability theorem to minimize the control effort and attenuate chattering. Performance comparisons with parallel control, relative coupling control and conventional PI control are investigated on a four-motor synchronization control system. Extensive simulation results show the effectiveness of the proposed control scheme.

  5. Modeling the Effect of Multiple Matrix Cracking Modes on Cyclic Hysteresis Loops of 2D Woven Ceramic-Matrix Composites

    NASA Astrophysics Data System (ADS)

    Longbiao, Li

    2016-08-01

    In this paper, the effect of multiple matrix cracking modes on cyclic loading/unloading hysteresis loops of 2D woven ceramic-matrix composites (CMCs) has been investigated. The interface slip between fibers and the matrix existed in matrix cracking mode 3 and mode 5, in which matrix cracking and interface debonding occurred in longitudinal yarns, are considered as the major reason for hysteresis loops of 2D woven CMCs. The effects of fiber volume content, peak stress, matrix crack spacing, interface properties, matrix cracking mode proportion and interface wear on interface slip and hysteresis loops have been analyzed. The cyclic loading/unloading hysteresis loops of 2D woven SiC/SiC composite corresponding to different peak stresses have been predicted using the present analysis. It was found that the damage parameter, i.e., the proportion of matrix cracking mode 3 in the entire cracking modes of the composite, increases with increasing peak stress.

  6. Sliding-mode control of single input multiple output DC-DC converter

    NASA Astrophysics Data System (ADS)

    Zhang, Libo; Sun, Yihan; Luo, Tiejian; Wan, Qiyang

    2016-10-01

    Various voltage levels are required in the vehicle mounted power system. A conventional solution is to utilize an independent multiple output DC-DC converter whose cost is high and control scheme is complicated. In this paper, we design a novel SIMO DC-DC converter with sliding mode controller. The proposed converter can boost the voltage of a low-voltage input power source to a controllable high-voltage DC bus and middle-voltage output terminals, which endow the converter with characteristics of simple structure, low cost, and convenient control. In addition, the sliding mode control (SMC) technique applied in our converter can enhance the performances of a certain SIMO DC-DC converter topology. The high-voltage DC bus can be regarded as the main power source to the high-voltage facility of the vehicle mounted power system, and the middle-voltage output terminals can supply power to the low-voltage equipment on an automobile. In the respect of control algorithm, it is the first time to propose the SMC-PID (Proportion Integration Differentiation) control algorithm, in which the SMC algorithm is utilized and the PID control is attended to the conventional SMC algorithm. The PID control increases the dynamic ability of the SMC algorithm by establishing the corresponding SMC surface and introducing the attached integral of voltage error, which endow the sliding-control system with excellent dynamic performance. At last, we established the MATLAB/SIMULINK simulation model, tested performance of the system, and built the hardware prototype based on Digital Signal Processor (DSP). Results show that the sliding mode control is able to track a required trajectory, which has robustness against the uncertainties and disturbances.

  7. Sliding-mode control of single input multiple output DC-DC converter.

    PubMed

    Zhang, Libo; Sun, Yihan; Luo, Tiejian; Wan, Qiyang

    2016-10-01

    Various voltage levels are required in the vehicle mounted power system. A conventional solution is to utilize an independent multiple output DC-DC converter whose cost is high and control scheme is complicated. In this paper, we design a novel SIMO DC-DC converter with sliding mode controller. The proposed converter can boost the voltage of a low-voltage input power source to a controllable high-voltage DC bus and middle-voltage output terminals, which endow the converter with characteristics of simple structure, low cost, and convenient control. In addition, the sliding mode control (SMC) technique applied in our converter can enhance the performances of a certain SIMO DC-DC converter topology. The high-voltage DC bus can be regarded as the main power source to the high-voltage facility of the vehicle mounted power system, and the middle-voltage output terminals can supply power to the low-voltage equipment on an automobile. In the respect of control algorithm, it is the first time to propose the SMC-PID (Proportion Integration Differentiation) control algorithm, in which the SMC algorithm is utilized and the PID control is attended to the conventional SMC algorithm. The PID control increases the dynamic ability of the SMC algorithm by establishing the corresponding SMC surface and introducing the attached integral of voltage error, which endow the sliding-control system with excellent dynamic performance. At last, we established the MATLAB/SIMULINK simulation model, tested performance of the system, and built the hardware prototype based on Digital Signal Processor (DSP). Results show that the sliding mode control is able to track a required trajectory, which has robustness against the uncertainties and disturbances.

  8. Chitinase from Autographa californica multiple nucleopolyhedrovirus: rapid purification from Sf-9 medium and mode of action.

    PubMed

    Fukamizo, Tamo; Sato, Hirokazu; Mizuhara, Mamiko; Ohnuma, Takayuki; Gotoh, Takeshi; Hiwatashi, Kazuyuki; Takahashi, Saori

    2011-01-01

    Autographa californica multiple nucleopolyhedrovirus (AcMNPV) chitinase is involved in the final liquefaction of infected host larvae. We purified the chitinase rapidly to homogeneity from Sf-9 cells infected with AcMNPV by a simple procedure using a pepstatin-aminohexyl-Sepharose column. In past studies, a recombinant AcMNPV chitinase was found to exhibit both exo- and endo-chitinase activities by analysis using artificial substrates with a fluorescent probe. In this study, however, we obtained more accurate information on the mode of action of the chitinase by HPLC analysis of the enzymatic products using natural oligosaccharide and polysaccharide substrates. The AcMNPV chitinase hydrolyzed the second β-1,4 glycosidic linkage from the non-reducing end of the chitin oligosaccharide substrates [(GlcNAc)(n), n=4, 5, and 6], producing the β-anomer of (GlcNAc)₂. The mode of action was similar to that of Serratia marcescens chitinase A (SmChiA), the amino acid sequence of which is 60.5% homologous to that of the AcMNPV enzyme. The enzyme also hydrolyzed solid β-chitin, producing only (GlcNAc)₂. The AcMNPV chitinase processively hydrolyzes solid β-chitin in a manner similar to SmChiA. The processive mechanism of the enzyme appears to be advantageous in liquefaction of infected host larvae.

  9. Multiple Modes of Action of the Squamocin in the Midgut Cells of Aedes aegypti Larvae

    PubMed Central

    de Paula, Sérgio Oliveira; Martins, Gustavo Ferreira; Zanuncio, José Cola

    2016-01-01

    Annonaceous acetogenins are botanical compounds with good potential for use as insecticides. In the vector, Aedes aegypti (L.) (Diptera: Culicidae), squamocin (acetogenin) has been reported to be a larvicide and cytotoxic, but the modes of action of this molecule are still poorly understood. This study evaluated the changes in the cell morphology, and in the expression of genes, for autophagy (Atg1 and Atg8), for membrane ion transporter V-ATPase, and for water channel aquaporin-4 (Aqp4) in the midgut of A. aegypti larvae exposed to squamocin from Annona mucosa Jacq. (Annonaceae). Squamocin showed cytotoxic action with changes in the midgut epithelium and digestive cells of A. aegypti larvae, increase in the expression for autophagy gene Atg1 and Atg8, decrease in the expression of V-ATPase, decrease in the expression of Aqp4 gene in LC20 and inhibition of Apq4 genes in the midgut of this vector in LC50. These multiple modes of action for squamocin are described for the first time in insects, and they are important because different sites of action of squamocin from A. mucosa may reduce the possibility of resistance of A. aegypti to this molecule. PMID:27532504

  10. Probiotics as beneficial microbes in aquaculture: an update on their multiple modes of action: a review.

    PubMed

    Zorriehzahra, Mohammad Jalil; Delshad, Somayeh Torabi; Adel, Milad; Tiwari, Ruchi; Karthik, K; Dhama, Kuldeep; Lazado, Carlo C

    2016-12-01

    Wide and discriminate use of antibiotics has resulted in serious biological and ecological concerns, especially the emergence of antibiotic resistance. Probiotics, known as beneficial microbes, are being proposed as an effective and eco-friendly alternative to antibiotics. They were first applied in aquaculture species more than three decades ago, but considerable attention had been given only in the early 2000s. Probiotics are defined as live or dead, or even a component of the microorganisms that act under different modes of action in conferring beneficial effects to the host or to its environment. Several probiotics have been characterized and applied in fish and a number of them are of host origin. Unlike some disease control alternatives being adapted and proposed in aquaculture where actions are unilateral, the immense potential of probiotics lies on their multiple mechanisms in conferring benefits to the host fish and the rearing environment. The staggering number of probiotics papers in aquaculture highlights the multitude of advantages from these microorganisms and conspicuously position them in the dynamic search for health-promoting alternatives for cultured fish. This paper provides an update on the use of probiotics in finfish aquaculture, particularly focusing on their modes of action. It explores the contemporary understanding of their spatial and nutritional competitiveness, inhibitory metabolites, environmental modification capability, immunomodulatory potential and stress-alleviating mechanism. This timely update affirms the importance of probiotics in fostering sustainable approaches in aquaculture and provides avenues in furthering its research and development.

  11. A comprehensive approach to ascertain the binding mode of curcumin with DNA.

    PubMed

    Haris, P; Mary, Varughese; Aparna, P; Dileep, K V; Sudarsanakumar, C

    2017-03-15

    Curcumin is a natural phytochemical from the rhizoma of Curcuma longa, the popular Indian spice that exhibits a wide range of pharmacological properties like antioxidant, anticancer, anti-inflammatory, antitumor, and antiviral activities. In the published literatures we can see different studies and arguments on the interaction of curcumin with DNA. The intercalative binding, groove binding and no binding of curcumin with DNA were reported. In this context, we conducted a detailed study to understand the mechanism of recognition of dimethylsulfoxide-solubilized curcumin by DNA. The interaction of curcumin with calf thymus DNA (ctDNA) was confirmed by agarose gel electrophoresis. The nature of binding and energetics of interaction were studied by Isothermal Titration Calorimetry (ITC), Differential Scanning Calorimetry (DSC), UV-visible, fluorescence and melting temperature (Tm) analysis. The experimental data were compared with molecular modeling studies. Our investigation confirmed that dimethylsulfoxide-solubilized curcumin binds in the minor groove of the ctDNA without causing significant structural alteration to the DNA.

  12. The complex binding mode of the peptide hormone H2 relaxin to its receptor RXFP1

    PubMed Central

    Sethi, Ashish; Bruell, Shoni; Patil, Nitin; Hossain, Mohammed Akhter; Scott, Daniel J.; Petrie, Emma J.; Bathgate, Ross A. D.; Gooley, Paul R.

    2016-01-01

    H2 relaxin activates the relaxin family peptide receptor-1 (RXFP1), a class A G-protein coupled receptor, by a poorly understood mechanism. The ectodomain of RXFP1 comprises an N-terminal LDLa module, essential for activation, tethered to a leucine-rich repeat (LRR) domain by a 32-residue linker. H2 relaxin is hypothesized to bind with high affinity to the LRR domain enabling the LDLa module to bind and activate the transmembrane domain of RXFP1. Here we define a relaxin-binding site on the LDLa-LRR linker, essential for the high affinity of H2 relaxin for the ectodomain of RXFP1, and show that residues within the LDLa-LRR linker are critical for receptor activation. We propose H2 relaxin binds and stabilizes a helical conformation of the LDLa-LRR linker that positions residues of both the linker and the LDLa module to bind the transmembrane domain and activate RXFP1. PMID:27088579

  13. A comprehensive approach to ascertain the binding mode of curcumin with DNA

    NASA Astrophysics Data System (ADS)

    Haris, P.; Mary, Varughese; Aparna, P.; Dileep, K. V.; Sudarsanakumar, C.

    2017-03-01

    Curcumin is a natural phytochemical from the rhizoma of Curcuma longa, the popular Indian spice that exhibits a wide range of pharmacological properties like antioxidant, anticancer, anti-inflammatory, antitumor, and antiviral activities. In the published literatures we can see different studies and arguments on the interaction of curcumin with DNA. The intercalative binding, groove binding and no binding of curcumin with DNA were reported. In this context, we conducted a detailed study to understand the mechanism of recognition of dimethylsulfoxide-solubilized curcumin by DNA. The interaction of curcumin with calf thymus DNA (ctDNA) was confirmed by agarose gel electrophoresis. The nature of binding and energetics of interaction were studied by Isothermal Titration Calorimetry (ITC), Differential Scanning Calorimetry (DSC), UV-visible, fluorescence and melting temperature (Tm) analysis. The experimental data were compared with molecular modeling studies. Our investigation confirmed that dimethylsulfoxide-solubilized curcumin binds in the minor groove of the ctDNA without causing significant structural alteration to the DNA.

  14. Binding modes of decavanadate to myosin and inhibition of the actomyosin ATPase activity.

    PubMed

    Tiago, Teresa; Martel, Paulo; Gutiérrez-Merino, Carlos; Aureliano, Manuel

    2007-04-01

    Decavanadate, a vanadate oligomer, is known to interact with myosin and to inhibit the ATPase activity, but the putative binding sites and the mechanism of inhibition are still to be clarified. We have previously proposed that the decavanadate (V(10)O(28)(6-)) inhibition of the actin-stimulated myosin ATPase activity is non-competitive towards both actin and ATP. A likely explanation for these results is that V(10) binds to the so-called back-door at the end of the Pi-tube opposite to the nucleotide-binding site. In order to further investigate this possibility, we have carried out molecular docking simulations of the V(10) oligomer on three different structures of the myosin motor domain of Dictyostelium discoideum, representing distinct states of the ATPase cycle. The results indicate a clear preference of V(10) to bind at the back-door, but only on the "open" structures where there is access to the phosphate binding-loop. It is suggested that V(10) acts as a "back-door stop" blocking the closure of the 50-kDa cleft necessary to carry out ATP-gamma-phosphate hydrolysis. This provides a simple explanation to the non-competitive behavior of V(10) and spurs the use of the oligomer as a tool to elucidate myosin back-door conformational changes in the process of muscle contraction.

  15. Structure of bacterial transcription factor SpoIIID and evidence for a novel mode of DNA binding.

    PubMed

    Chen, Bin; Himes, Paul; Liu, Yu; Zhang, Yang; Lu, Zhenwei; Liu, Aizhuo; Yan, Honggao; Kroos, Lee

    2014-06-01

    SpoIIID is evolutionarily conserved in endospore-forming bacteria, and it activates or represses many genes during sporulation of Bacillus subtilis. An SpoIIID monomer binds DNA with high affinity and moderate sequence specificity. In addition to a predicted helix-turn-helix motif, SpoIIID has a C-terminal basic region that contributes to DNA binding. The nuclear magnetic resonance (NMR) solution structure of SpoIIID in complex with DNA revealed that SpoIIID does indeed have a helix-turn-helix domain and that it has a novel C-terminal helical extension. Residues in both of these regions interact with DNA, based on the NMR data and on the effects on DNA binding in vitro of SpoIIID with single-alanine substitutions. These data, as well as sequence conservation in SpoIIID binding sites, were used for information-driven docking to model the SpoIIID-DNA complex. The modeling resulted in a single cluster of models in which the recognition helix of the helix-turn-helix domain interacts with the major groove of DNA, as expected. Interestingly, the C-terminal extension, which includes two helices connected by a kink, interacts with the adjacent minor groove of DNA in the models. This predicted novel mode of binding is proposed to explain how a monomer of SpoIIID achieves high-affinity DNA binding. Since SpoIIID is conserved only in endospore-forming bacteria, which include important pathogenic Bacilli and Clostridia, whose ability to sporulate contributes to their environmental persistence, the interaction of the C-terminal extension of SpoIIID with DNA is a potential target for development of sporulation inhibitors.

  16. Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor

    NASA Astrophysics Data System (ADS)

    Anighoro, Andrew; Bajorath, Jürgen

    2016-06-01

    We report an investigation designed to explore alternative approaches for ranking of docking poses in the search for antagonists of the adenosine A2A receptor, an attractive target for structure-based virtual screening. Calculation of 3D similarity of docking poses to crystallographic ligand(s) as well as similarity of receptor-ligand interaction patterns was consistently superior to conventional scoring functions for prioritizing antagonists over decoys. Moreover, the use of crystallographic antagonists and agonists, a core fragment of an antagonist, and a model of an agonist placed into the binding site of an antagonist-bound form of the receptor resulted in a significant early enrichment of antagonists in compound rankings. Taken together, these findings showed that the use of binding modes of agonists and/or antagonists, even if they were only approximate, for similarity assessment of docking poses or comparison of interaction patterns increased the odds of identifying new active compounds over conventional scoring.

  17. Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data.

    PubMed Central

    Brandstetter, H.; Engh, R. A.; Von Roedern, E. G.; Moroder, L.; Huber, R.; Bode, W.; Grams, F.

    1998-01-01

    Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases, which have been implicated in various disease processes. Various classes of MMP inhibitors, including hydroxamic acids, phosphinic acids, and thiols, have been previously described. Most of these mimic peptides, and most likely bind analogous to the corresponding peptide substrates. Among the hydroxamic acids, malonic acid derivatives have been used as MMP inhibitors, although optimization of their inhibition potency was not successful. Here we report the design of malonic acid-based inhibitors using the X-ray structure of a collagenase/inhibitor complex, which revealed a nonsubstrate-like binding mode. The proposed beta-type turn-like conformation for the improved inhibitors was confirmed by X-ray crystallography. The observation of nonsubstrate-like binding confirms the original strategy for structure-based modeling of improved malonic acid inhibitors, and explains kinetic data that are inconsistent with substrate-like binding. Detailed interactions for the improved inhibitors seen in the crystal structure also suggest possibilities for further modifications in cycles of structure based drug design. Indeed, we have designed nonpeptidic inhibitors with approximately 500-fold improved inhibition based on these structures. PMID:9655333

  18. Quest for the binding mode of tetrabromobisphenol A with Calf thymus DNA

    NASA Astrophysics Data System (ADS)

    Wang, Yan-Qing; Zhang, Hong-Mei; Cao, Jian

    2014-10-01

    The binding interaction of tetrabromobisphenol A with Calf thymus DNA was studied by multi-spectroscopic and molecular modeling methods. The UV-vis study revealed that an obvious interaction between tetrabromobisphenol A and Calf thymus DNA happened. The π-π∗ transitions and the electron cloud of tetrabromobisphenol A might be changed by entering the groove of Calf thymus DNA. From the fluorescence spectral and thermodynamics studies, it was concluded that the hydrogen bonds and hydrophobic force played a major role in the binding of tetrabromobisphenol A to Calf thymus DNA. The molecular modeling study showed that the possible sites of tetrabromobisphenol A in the groove of DNA. Circular dichroism study also depicted that tetrabromobisphenol A bond to DNA. These above results would further advance our knowledge on the molecular mechanism of the binding interactions of brominated flame-retardants with nucleic acid.

  19. Specificity profiling of dual specificity phosphatase vaccinia VH1-related (VHR) reveals two distinct substrate binding modes.

    PubMed

    Luechapanichkul, Rinrada; Chen, Xianwen; Taha, Hashem A; Vyas, Shubham; Guan, Xiaoyan; Freitas, Michael A; Hadad, Christopher M; Pei, Dehua

    2013-03-01

    Vaccinia VH1-related (VHR) is a dual specificity phosphatase that consists of only a single catalytic domain. Although several protein substrates have been identified for VHR, the elements that control the in vivo substrate specificity of this enzyme remain unclear. In this work, the in vitro substrate specificity of VHR was systematically profiled by screening combinatorial peptide libraries. VHR exhibits more stringent substrate specificity than classical protein-tyrosine phosphatases and recognizes two distinct classes of Tyr(P) peptides. The class I substrates are similar to the Tyr(P) motifs derived from the VHR protein substrates, having sequences of (D/E/ϕ)(D/S/N/T/E)(P/I/M/S/A/V)pY(G/A/S/Q) or (D/E/ϕ)(T/S)(D/E)pY(G/A/S/Q) (where ϕ is a hydrophobic amino acid and pY is phosphotyrosine). The class II substrates have the consensus sequence of (V/A)P(I/L/M/V/F)X1-6pY (where X is any amino acid) with V/A preferably at the N terminus of the peptide. Site-directed mutagenesis and molecular modeling studies suggest that the class II peptides bind to VHR in an opposite orientation relative to the canonical binding mode of the class I substrates. In this alternative binding mode, the Tyr(P) side chain binds to the active site pocket, but the N terminus of the peptide interacts with the carboxylate side chain of Asp(164), which normally interacts with the Tyr(P) + 3 residue of a class I substrate. Proteins containing the class II motifs are efficient VHR substrates in vitro, suggesting that VHR may act on a novel class of yet unidentified Tyr(P) proteins in vivo.

  20. Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO.

    PubMed

    Raghavendra, S; Aditya Rao, S J; Kumar, Vadlapudi; Ramesh, C K

    2015-12-01

    Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the protein Polyphenoloxidase (PPO). The protein was isolated from Mucuna pruriens and confirmed as tyrosinases involved in L-DOPA production. The activity was measured using different inhibitors at different concentrations taking catechol as substrate. A high-throughput binding study was conducted to compare the binding orientations of individual ligands and multiple ligands employing Autodock 4.2. The results of single substrate docking showed a better binding of urea with the binding energy of -3.48 kJ mol(-1) and inter molecular energy of -3.48 kJ mol(-1) while the results of MLSD revealed that ascorbic acid combined with the substrate showed better inhibition with a decreased binding energy of -2.37 kJ mol(-1).

  1. DNA binding, DNA cleavage and cytotoxicity studies of a new water soluble copper(II) complex: The effect of ligand shape on the mode of binding

    NASA Astrophysics Data System (ADS)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Roshanfekr, Hamideh; Shahabadi, Nahid; Mansouri, Ghobad

    2012-02-01

    The interaction of native calf thymus DNA (CT-DNA) with [Cu(ph 2phen)(phen-dione)Cl]Cl was studied at physiological pH by spectrophotometric, spectrofluorometric, circular dichroism, and viscometric techniques. Considerable hypochromicity and red shift are observed in the UV absorption band of the Cu complex. Binding constants ( Kb) of DNA with the complex were calculated at different temperatures. Thermodynamic parameters, enthalpy and entropy changes were calculated according to Van't Hoff equation, which indicated that reaction is predominantly enthalpically driven. All these results indicate that Cu(II) complex interacts with CT-DNA via intercalative mode. Also, this new complex induced cleavage in pUC18 plasmid DNA as indicated in gel electrophoresis and showed excellent antitumor activity against K562 (human chronic myeloid leukemia) and human T lymphocyte carcinoma-Jurkat cell lines.

  2. Multiple omnidirectional defect modes and nonlinear magnetic-field effects in metamaterial photonic superlattices with a polaritonic defect

    NASA Astrophysics Data System (ADS)

    Robles-Uriza, A. X.; Reyes Gómez, F.; Mejía-Salazar, J. R.

    2016-09-01

    We report the existence of multiple omnidirectional defect modes in the zero-nbar gap of photonic stacks, made of alternate layers of conventional dielectric and double-negative metamaterial, with a polaritonic defect layer. In the case of nonlinear magnetic metamaterials, the optical bistability phenomenon leads to switching from negligible to perfect transmission around these defect modes. We hope these findings have potential applications in the design and development of multichannel optical filters, power limiters, optical-diodes and optical-transistors.

  3. RANKL employs distinct binding modes to engage RANK and the osteoprotegerin decoy receptor.

    PubMed

    Nelson, Christopher A; Warren, Julia T; Wang, Michael W-H; Teitelbaum, Steven L; Fremont, Daved H

    2012-11-07

    Osteoprotegerin (OPG) and receptor activator of nuclear factor κB (RANK) are members of the tumor necrosis factor receptor (TNFR) superfamily that regulate osteoclast formation and function by competing for RANK ligand (RANKL). RANKL promotes osteoclast development through RANK activation, while OPG inhibits this process by sequestering RANKL. For comparison, we solved crystal structures of RANKL with RANK and RANKL with OPG. Complementary biochemical and functional studies reveal that the monomeric cytokine-binding region of OPG binds RANKL with ∼500-fold higher affinity than RANK and inhibits RANKL-stimulated osteoclastogenesis ∼150 times more effectively, in part because the binding cleft of RANKL makes unique contacts with OPG. Several side chains as well as the C-D and D-E loops of RANKL occupy different orientations when bound to OPG versus RANK. High affinity OPG binding requires a 90s loop Phe residue that is mutated in juvenile Paget's disease. These results suggest cytokine plasticity may help to fine-tune specific tumor necrosis factor (TNF)-family cytokine/receptor pair selectivity.

  4. PEPTIDE BINDING AS A MODE OF ACTION FOR THE CARCINOGENICITY AND TOXICITY OF ARSENIC

    EPA Science Inventory

    Arsenic exposure leads to tumors in human skin, lung, urinary bladder, kidney and liver. Three likely initial stages of arsenical-macromolecular interaction are (1) binding of trivalent arsenicals to the sulfhydryl groups of peptides and proteins, (2) arsenical-induced generation...

  5. MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode

    PubMed Central

    Wagner, Tristan; Ermler, Ulrich; Shima, Seigo

    2016-01-01

    In the three domains of life, vitamin B12 (cobalamin) is primarily used in methyltransferase and isomerase reactions. The methyltransferase complex MtrA–H of methanogenic archaea has a key function in energy conservation by catalysing the methyl transfer from methyl-tetrahydromethanopterin to coenzyme M and its coupling with sodium-ion translocation. The cobalamin-binding subunit MtrA is not homologous to any known B12-binding proteins and is proposed as the motor of the sodium-ion pump. Here, we present crystal structures of the soluble domain of the membrane-associated MtrA from Methanocaldococcus jannaschii and the cytoplasmic MtrA homologue/cobalamin complex from Methanothermus fervidus. The MtrA fold corresponds to the Rossmann-type α/β fold, which is also found in many cobalamin-containing proteins. Surprisingly, the cobalamin-binding site of MtrA differed greatly from all the other cobalamin-binding sites. Nevertheless, the hydrogen-bond linkage at the lower axial-ligand site of cobalt was equivalently constructed to that found in other methyltransferases and mutases. A distinct polypeptide segment fixed through the hydrogen-bond linkage in the relaxed Co(III) state might be involved in propagating the energy released upon corrinoid demethylation to the sodium-translocation site by a conformational change. PMID:27324530

  6. Multiple antigen peptide dendrimer elicits antibodies for detecting rat and mouse growth hormone binding proteins

    PubMed Central

    Aguilar, Roberto M.; Talamantes, Frank J.; Bustamante, Juan J.; Muñoz, Jesus; Treviño, Lisa R.; Martinez, Andrew O.; Haro, Luis S.

    2009-01-01

    The membrane-bound rat growth hormone receptor (GH-R) and an alternatively spliced isoform, the soluble rat GH binding protein (GH-BP), are comprised of identical N-terminal GH binding domains, however, their C-terminal sequences differ. Immunological reagents are needed to distinguish between the two isoforms in order to understand their respective roles in mediating the actions of GH. Accordingly, a tetravalent multiple antigen peptide (MAP) dendrimer with four identical branches of a C-terminal peptide sequence of the rat GH-BP (GH-BP263-279) was synthesized and used as an immunogen in rabbits. Solid-phase peptide synthesis of four GH-BP263-279 segments onto a tetravalent Lys2-Lys-β-Ala-OH core peptide was carried out using N-(9-fluorenyl)methoxycarbonyl chemistry. The mass of the RP-HPLC purified synthetic product, 8398 Da, determined by ESI-MS, was identical to expected mass. Three anti-rat GH-BP263-279 MAP antisera, BETO-8039, BETO-8040 and BETO-8041, at dilutions of 10-3, recognized both the rat GH-BP263-279 MAP and recombinant mouse GH-BP with ED50s within a range of 5-10 fmol but did not cross-react with BSA in dot blot analyses. BETO-8041 antisera (10-3 dilution) recognized GH-BPs of rat serum and liver having Mrs ranging from 35-130 kDa but did not recognize full-length rat GH-Rs. The antisera also detected recombinant mouse GH-BPs. In summary, the tetravalent rat GH-BP263-279 MAP dendrimer served as an effective immunogenic antigen in eliciting high titer antisera specific for the C-termini of both rat and mouse GH-BPs. The antisera will facilitate studies aimed at improving our understanding of the biology of GH-BPs. PMID:19089805

  7. Interaction of the N-(3-Methylpyridin-2-yl)amide Derivatives of Flurbiprofen and Ibuprofen with FAAH: Enantiomeric Selectivity and Binding Mode

    PubMed Central

    Deplano, Alessandro; Smaldone, Giovanni; Pedone, Emilia; Luque, F. Javier; Svensson, Mona; Novellino, Ettore; Congiu, Cenzo; Onnis, Valentina; Catalanotti, Bruno; Fowler, Christopher J.

    2015-01-01

    Background Combined fatty acid amide hydrolase (FAAH) and cyclooxygenase (COX) inhibition is a promising approach for pain-relief. The Flu-AM1 and Ibu-AM5 derivatives of flurbiprofen and ibuprofen retain similar COX-inhibitory properties and are more potent inhibitors of FAAH than the parent compounds. However, little is known as to the nature of their interaction with FAAH, or to the importance of their chirality. This has been explored here. Methodology/Principal Findings FAAH inhibitory activity was measured in rat brain homogenates and in lysates expressing either wild-type or FAAHT488A-mutated enzyme. Molecular modelling was undertaken using both docking and molecular dynamics. The (R)- and (S)-enantiomers of Flu-AM1 inhibited rat FAAH with similar potencies (IC50 values of 0.74 and 0.99 μM, respectively), whereas the (S)-enantiomer of Ibu-AM5 (IC50 0.59 μM) was more potent than the (R)-enantiomer (IC50 5.7 μM). Multiple inhibition experiments indicated that both (R)-Flu-AM1 and (S)-Ibu-AM5 inhibited FAAH in a manner mutually exclusive to carprofen. Computational studies indicated that the binding site for the Flu-AM1 and Ibu-AM5 enantiomers was located between the acyl chain binding channel and the membrane access channel, in a site overlapping the carprofen binding site, and showed a binding mode in line with that proposed for carprofen and other non-covalent ligands. The potency of (R)-Flu-AM1 was lower towards lysates expressing FAAH mutated at the proposed carprofen binding area than in lysates expressing wild-type FAAH. Conclusions/Significance The study provides kinetic and structural evidence that the enantiomers of Flu-AM1 and Ibu-AM5 bind in the substrate channel of FAAH. This information will be useful in aiding the design of novel dual-action FAAH: COX inhibitors. PMID:26565710

  8. Multiple Beam Correlation Using Single-Mode Fiber Optics with Application to Interferometric Imaging

    NASA Astrophysics Data System (ADS)

    Shaklan, Stuart Bruce

    A study of the application of single-mode fiber optics to the multiple-beam interferometric recombination problem is presented. In the laboratory, the fibers have been used in wide bandwidth, two-arm, Mach-Zehnder test interferometers as well as a 5-telescope imaging interferometer connected to an all-fiber beam combiner. Based upon these experiments and some theoretical studies it is shown that fiber optics and fiber optic components such as directional couplers provide an excellent alternative to conventional optics such as mirrors, beamsplitters, and relay lenses. The equations describing the measurement of the complex degree of coherence in an interferometer with a single-mode fiber in each arm are derived. The equations reveal an important feature of the fibers: they filter phase fluctuations due to aberrations and turbulence at the input and convert them to intensity fluctuations at the output. This leads to a simplification of the calibration of measured visibilities. The coupling efficiency of light which has passed through a turbulent atmosphere is also studied as a function of fiber parameters and turbulence conditions for both image motion stabilized and non-stabilized cases. For the former case, coupling efficiency remains greater than 50% as long as telescope diameter is no larger than the turbulence coherence length. Beam combination architectures using arrays of directional couplers are fully discussed. Arrays accommodating up to 20 input beams are presented. The arrays require only N detector pixels for N input beams. A scheme of temporal multiplexing of the phase of each beam is used to identify individual fringe pairs. One possible scheme allows wide bandwidths even for large numbers of beams. A 5-telescope interferometer has been constructed and connected to an all-fiber beam combiner. Two extended objects were observed and reconstructed using standard radio astronomy VLBI software. The interferometer and beam combiner had good thermal and

  9. Identification, pharmacological evaluation and binding mode analysis of novel chromene and chromane based σ1 receptor ligands.

    PubMed

    Laurini, Erik; Harel, Dipak; Marson, Domenico; Schepmann, Dirk; Schmidt, Thomas J; Pricl, Sabrina; Wünsch, Bernhard

    2014-08-18

    A set of aminoethyl substituted chromenes 3 and chromanes 4, originally developed as antiprotozoal drugs was evaluated as novel types of σ1 receptor ligands. Analysis of SAR showed that chromenes 3 have a higher σ1 affinity than chromanes 4. A distance of four bond lengths between the basic amino moiety and the phenyl ring (3c), an alicyclic N-substituent such as the cyclohexylmethyl moiety (3l), and methylation of the secondary amine to afford a tertiary amine (3n) result in very high σ1 affinity and selectivity over the σ2 subtype. Compounds 3a-n and 4a-e were docked into the putative binding site of the σ1 receptor model and the relevant binding mode was analyzed and scored. Specifically, for the best σ1 ligand 3n, a salt bridge between Asp126 and the protonated amino group, an H-bond between the receptor backbone NH group (Ala122-Glu123) and the methoxy moiety of 3n, a lipophilic protein cavity encasing the chromene ring, and a T-shaped π-π stacking between the indole ring of Trp121 and the phenyl ring of 3n represent the most important ligand/protein stabilizing interactions. The binding pose of 3n was compared with the binding poses of the non-methylated chromene 3c, the saturated chromane 4c, and the N-cyclohexylmethyl derivative 3l. The contribution of the single amino acids to the overall free binding enthalpy was analyzed.

  10. The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana

    PubMed Central

    Zemlyanskaya, Elena V.; Levitsky, Victor G.; Oshchepkov, Dmitry Y.; Grosse, Ivo; Mironova, Victoria V.

    2017-01-01

    The plant hormone ethylene regulates numerous developmental processes and stress responses. Ethylene signaling proceeds via a linear pathway, which activates transcription factor (TF) EIN3, a primary transcriptional regulator of ethylene response. EIN3 influences gene expression upon binding to a specific sequence in gene promoters. This interaction, however, might be considerably affected by additional co-factors. In this work, we perform whole genome bioinformatics study to identify the impact of epigenetic factors in EIN3 functioning. The analysis of publicly available ChIP-Seq data on EIN3 binding in Arabidopsis thaliana showed bimodality of distribution of EIN3 binding regions (EBRs) in gene promoters. Besides a sharp peak in close proximity to transcription start site, which is a common binding region for a wide variety of TFs, we found an additional extended peak in the distal promoter region. We characterized all EBRs with respect to the epigenetic status appealing to previously published genome-wide map of nine chromatin states in A. thaliana. We found that the implicit distal peak was associated with a specific chromatin state (referred to as chromatin state 4 in the primary source), which was just poorly represented in the pronounced proximal peak. Intriguingly, EBRs corresponding to this chromatin state 4 were significantly associated with ethylene response, unlike the others representing the overwhelming majority of EBRs related to the explicit proximal peak. Moreover, we found that specific EIN3 binding sequences predicted with previously described model were enriched in the EBRs mapped to the chromatin state 4, but not to the rest ones. These results allow us to conclude that the interplay of genetic and epigenetic factors might cause the distinct modes of EIN3 regulation. PMID:28119721

  11. Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis.

    PubMed

    Chi, Gamma; Manos-Turvey, Alexandra; O'Connor, Patrick D; Johnston, Jodie M; Evans, Genevieve L; Baker, Edward N; Payne, Richard J; Lott, J Shaun; Bulloch, Esther M M

    2012-06-19

    MbtI is the salicylate synthase that catalyzes the first committed step in the synthesis of the iron chelating compound mycobactin in Mycobacterium tuberculosis. We previously developed a series of aromatic inhibitors against MbtI based on the reaction intermediate for this enzyme, isochorismate. The most potent of these inhibitors had hydrophobic substituents, ranging in size from a methyl to a phenyl group, appended to the terminal alkene of the enolpyruvyl group. These compounds exhibited low micromolar inhibition constants against MbtI and were at least an order of magnitude more potent than the parental compound for the series, which carries a native enolpyruvyl group. In this study, we sought to understand how the substituted enolpyruvyl group confers greater potency, by determining cocrystal structures of MbtI with six inhibitors from the series. A switch in binding mode at the MbtI active site is observed for inhibitors carrying a substituted enolpyruvyl group, relative to the parental compound. Computational studies suggest that the change in binding mode, and higher potency, is due to the effect of the substituents on the conformational landscape of the core inhibitor structure. The crystal structures and fluorescence-based thermal shift assays indicate that substituents larger than a methyl group are accommodated in the MbtI active site through significant but localized flexibility in the peptide backbone. These findings have implications for the design of improved inhibitors of MbtI, as well as other chorismate-utilizing enzymes from this family.

  12. Ultrafast photoelectron migration in dye-sensitized solar cells: Influence of the binding mode and many-body interactions

    NASA Astrophysics Data System (ADS)

    Hermann, G.; Tremblay, J. C.

    2016-11-01

    In the present contribution, the ultrafast photoinduced electron migration dynamics at the interface between an alizarin dye and an anatase TiO2 thin film is investigated from first principles. Comparison between a time-dependent many-electron configuration interaction ansatz and a single active electron approach sheds light on the importance of many-body effects, stemming from uniquely defined initial conditions prior to photoexcitation. Particular emphasis is put on understanding the influence of the binding mode on the migration process. The dynamics is analyzed on the basis of a recently introduced toolset in the form of electron yields, electronic fluxes, and flux densities, to reveal microscopic details of the electron migration mechanism. From the many-body perspective, insight into the nature of electron-electron and hole-hole interactions during the charge transfer process is obtained. The present results reveal that the single active electron approach yields quantitatively and phenomenologically similar results as the many-electron ansatz. Furthermore, the charge migration processes in the dye-TiO2 model clusters with different binding modes exhibit similar mechanistic pathways but on largely different time scales.

  13. Binding mode and potency of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors targeting Trypanosoma cruzi CYP51

    DOE PAGES

    Vieira, Debora F.; Choi, Jun Yong; Calvet, Claudia M.; ...

    2014-11-13

    Chagas disease is a chronic infection in humans caused by Trypanosoma cruzi and manifested in progressive cardiomyopathy and/or gastrointestinal dysfunction. Limited therapeutic options to prevent and treat Chagas disease put 8 million people infected with T. cruzi worldwide at risk. CYP51, involved in the biosynthesis of the membrane sterol component in eukaryotes, is a promising drug target in T. cruzi. We report the structure–activity relationships (SAR) of an N-arylpiperazine series of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors designed to probe the impact of substituents in the terminal N-phenyl ring on binding mode, selectivity and potency. Depending on the substituents at C-4, two distinct ringmore » binding modes, buried and solvent-exposed, have been observed by X-ray structure analysis (resolution of 1.95–2.48 Å). Lastly, the 5-chloro-substituted analogs 9 and 10 with no substituent at C-4 demonstrated improved selectivity and potency, suppressing ≥99.8% parasitemia in mice when administered orally at 25 mg/kg, b.i.d., for 4 days.« less

  14. Direct demonstration of unique mode of natural peptide binding to the type 2 cholecystokinin receptor using photoaffinity labeling.

    PubMed

    Dong, Maoqing; Miller, Laurence J

    2013-08-01

    Direct analysis of mode of peptide docking using intrinsic photoaffinity labeling has provided detailed insights for the molecular basis of cholecystokinin (CCK) interaction with the type 1 CCK receptor. In the current work, this technique has been applied to the closely related type 2 CCK receptor that also binds the natural full agonist peptide, CCK, with high affinity. A series of photolabile CCK analog probes with sites of covalent attachment extending from position 26 through 32 were characterized, with the highest affinity analogs that possessed full biological activity utilized in photoaffinity labeling. The position 29 probe, incorporating a photolabile benzoyl-phenylalanine in that position, was shown to bind with high affinity and to be a full agonist, with potency not different from that of natural CCK, and to covalently label the type 2 CCK receptor in a saturable, specific and efficient manner. Using proteolytic peptide mapping, mutagenesis, and radiochemical Edman degradation sequencing, this probe was shown to establish a covalent bond with type 2 CCK receptor residue Phe¹²⁰ in the first extracellular loop. This was in contrast to its covalent attachment to Glu³⁴⁵ in the third extracellular loop of the type 1 CCK receptor, directly documenting differences in mode of docking this peptide to these receptors.

  15. Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.

    PubMed Central

    Botos, I; Scapozza, L; Zhang, D; Liotta, L A; Meyer, E F

    1996-01-01

    Matrix metalloproteinase enzymes have been implicated in degenerative processes like tumor cell invasion, metastasis, and arthritis. Specific metalloproteinase inhibitors have been used to block tumor cell proliferation. We have examined the interaction of batimastat (BB-94) with a metalloproteinase [atrolysin C (Ht-d), EC 3.4.24.42] active site at 2.0-angstroms resolution (R = 16.8%). The title structure exhibits an unexpected binding geometry, with the thiophene ring deeply inserted into the primary specificity site. This unprecedented binding geometry dramatizes the significance of the cavernous primary specificity site, pointing the way for the design of a new generation of potential antitumor drugs. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8610113

  16. Biomolecular mode of action of metformin in relation to its copper binding properties.

    PubMed

    Repiščák, Peter; Erhardt, Stefan; Rena, Graham; Paterson, Martin J

    2014-02-04

    Metformin (Metf), the most commonly used type 2 diabetes drug, is known to affect the cellular housekeeping of copper. Recently, we discovered that the structurally closely related propanediimidamide (PDI) shows a cellular behavior different from that of Metf. Here we investigate the binding of these compounds to copper, to compare their binding strength. Furthermore, we take a closer look at the electronic properties of these compounds and their copper complexes such as molecular orbital interactions and electrostatic potential surfaces. Our results clearly show that the copper binding energies cannot alone be the cause of the biochemical differentiation between Metf and PDI. We conclude that other factors such as pKa values and hydrophilicity of the compounds play a crucial role in their cellular activity. Metf in contrast to PDI can occur as an anion in aqueous medium at moderate pH, forming much stronger complexes particularly with Cu(II) ions, suggesting that biguanides but not PDI may induce easy oxidation of Cu(I) ions extracted from proteins. The higher hydrophobicity and the lack of planarity of PDI may further differentiate it from biguanides in terms of their molecular recognition characteristics. These different properties could hold the key to metformin's mitochondrial activity because they suggest that the drug could act at least in part as a pro-oxidant of accessible protein-bound Cu(I) ions.

  17. Binding Mode Analysis of Zerumbone to Key Signal Proteins in the Tumor Necrosis Factor Pathway

    PubMed Central

    Fatima, Ayesha; Abdul, Ahmad Bustamam Hj.; Abdullah, Rasedee; Karjiban, Roghayeh Abedi; Lee, Vannajan Sanghiran

    2015-01-01

    Breast cancer is the second most common cancer among women worldwide. Several signaling pathways have been implicated as causative and progression agents. The tumor necrosis factor (TNF) α protein plays a dual role in promoting and inhibiting cancer depending largely on the pathway initiated by the binding of the protein to its receptor. Zerumbone, an active constituent of Zingiber zerumbet, Smith, is known to act on the tumor necrosis factor pathway upregulating tumour necrosis factor related apoptosis inducing ligand (TRAIL) death receptors and inducing apoptosis in cancer cells. Zerumbone is a sesquiterpene that is able to penetrate into the hydrophobic pockets of proteins to exert its inhibiting activity with several proteins. We found a good binding with the tumor necrosis factor, kinase κB (IKKβ) and the Nuclear factor κB (NF-κB) component proteins along the TNF pathway. Our results suggest that zerumbone can exert its apoptotic activities by inhibiting the cytoplasmic proteins. It inhibits the IKKβ kinase that activates the NF-κB and also binds to the NF-κB complex in the TNF pathway. Blocking both proteins can lead to inhibition of cell proliferating proteins to be downregulated and possibly ultimate induction of apoptosis. PMID:25629232

  18. Binding modes of phosphonic acid derivatives adsorbed on TiO2 surfaces: Assignments of experimental IR and NMR spectra based on DFT/PBC calculations

    NASA Astrophysics Data System (ADS)

    Geldof, D.; Tassi, M.; Carleer, R.; Adriaensens, P.; Roevens, A.; Meynen, V.; Blockhuys, F.

    2017-01-01

    A DFT study on the adsorption of a series of phosphonic acids (PAs) on the TiO2 anatase (101) and (001) surfaces was performed. The adsorption energies and geometries of the most stable binding modes were compared to literature data and the effect of the inclusion of dispersion forces in the energy calculations was gauged. As the (101) surface is the most exposed surface of TiO2 anatase, the calculated chemical shifts and vibrational frequencies of PAs adsorbed on this surface were compared to experimental 31P and 17O NMR and IR data in order to assign the two possible binding modes (mono- and bidentate) to peaks and bands in these spectra; due to the corrugated nature of anatase (101) tridentate binding is not possible on this surface. Analysis of the calculated and experimental 31P chemical shifts indicates that both monodentate and bidentate binding modes are present. For the reactive (001) surface, the results of the calculations indicate that both bi- and tridentate binding modes result in stable systems. Due to the particular sensitivity of 17O chemical shifts to hydrogen bonding and solvent effects, the model used is insufficient to assign these spectra at present. Comparison of calculated and experimental IR spectra leads to the conclusion that IR spectroscopy is not suitable for the characterization of the different binding modes of the adsorption complexes.

  19. Lipopolysaccharide Binding Protein and Oxidative Stress in a Multiple Sclerosis Model.

    PubMed

    Escribano, Begoña M; Medina-Fernández, Francisco J; Aguilar-Luque, Macarena; Agüera, Eduardo; Feijoo, Montserrat; Garcia-Maceira, Fe I; Lillo, Rafael; Vieyra-Reyes, Patricia; Giraldo, Ana I; Luque, Evelio; Drucker-Colín, René; Túnez, Isaac

    2017-01-01

    Recent findings in experimental autoimmune encephalomyelitis (EAE) suggest that altering certain bacterial populations present in the gut may lead to a proinflammatory condition, that could result in the development of multiple sclerosis (MS). Also, Reactive Oxygen Species seem to be involved in the course of MS. In this study, it has been aimed to relate all these variables starting from an analysis of the lipopolysaccharide (LPS) and LPS-binding protein (LBP) with the determination of parameters related to oxidative stress in the blood, brain and spinal cord. For this purpose, samples obtained from EAE rats and relapsing-remitting (RRMS) MS patients were used. In addition, EAE rats were treated with Natalizumab, N-acetyl-cysteine and dimethyl fumarate. Natalizumab was also employed in RRMS. The results of this study revealed an improvement in the clinical symptoms of the EAE and MS with the treatments, as well as a reduction in the oxidative stress parameters and in LBP. Correlations between the clinical variables of the disease, i.e. oxidative damage and LBP, were established. Although the conclusions of this research are indeed relevant, further investigation would be necessary to establish the intrinsic mechanisms of the MS-oxidative stress-microbiota relationship.

  20. Differential Detection of Tumor Cells Using a Combination of Cell Rolling, Multivalent Binding, and Multiple Antibodies

    PubMed Central

    2015-01-01

    Effective quantification and in situ identification of circulating tumor cells (CTCs) in blood are still elusive because of the extreme rarity and heterogeneity of the cells. In our previous studies, we developed a novel platform that captures tumor cells at significantly improved efficiency in vitro using a unique biomimetic combination of two physiological processes: E-selectin-induced cell rolling and poly(amidoamine) (PAMAM) dendrimer-mediated strong multivalent binding. Herein, we have engineered a novel multifunctional surface, on the basis of the biomimetic cell capture, through optimized incorporation of multiple antibodies directed to cancer cell-specific surface markers, such as epithelial cell adhesion molecule (EpCAM), human epidermal growth factor receptor-2 (HER-2), and prostate specific antigen (PSA). The surfaces were tested using a series of tumor cells, MDA-PCa-2b, MCF-7, and MDA-MB-361, both in mixture in vitro and after being spiked into human blood. Our multifunctional surface demonstrated highly efficient capture of tumor cells in human blood, achieving up to 82% capture efficiency (∼10-fold enhancement than a surface with the antibodies alone) and up to 90% purity. Furthermore, the multipatterned antibodies allowed differential capturing of the tumor cells. These results support that our multifunctional surface has great potential as an effective platform that accommodates virtually any antibodies, which will likely lead to clinically significant, differential detection of CTCs that are rare and highly heterogeneous. PMID:24892731

  1. Mode of binding of methyl acceptor substrates to the adrenaline-synthesizing enzyme phenylethanolamine N-methyltransferase: implications for catalysis.

    PubMed

    Gee, Christine L; Tyndall, Joel D A; Grunewald, Gary L; Wu, Qian; McLeish, Michael J; Martin, Jennifer L

    2005-12-27

    Here we report three crystal structure complexes of human phenylethanolamine N-methyltransferase (PNMT), one bound with a substrate that incorporates a flexible ethanolamine side chain (p-octopamine), a second bound with a semirigid analogue substrate [cis-(1R,2S)-2-amino-1-tetralol, cis-(1R,2S)-AT], and a third with trans-(1S,2S)-2-amino-1-tetralol [trans-(1S,2S)-AT] that acts as an inhibitor of PNMT rather than a substrate. A water-mediated interaction between the critical beta-hydroxyl of the flexible ethanolamine group of p-octopamine and an acidic residue, Asp267, is likely to play a key role in positioning the side chain correctly for methylation to occur at the amine. A second interaction with Glu219 may play a lesser role. Catalysis likely occurs via deprotonation of the amine through the action of Glu185; mutation of this residue significantly reduced the kcat without affecting the Km. The mode of binding of cis-(1R,2S)-AT supports the notion that this substrate is a conformationally restrained analogue of flexible PNMT substrates, in that it forms interactions with the enzyme similar to those observed for p-octopamine. By contrast, trans-(1S,2S)-AT, an inhibitor rather than a substrate, binds in an orientation that is flipped by 180 degrees compared with cis-(1R,2S)-AT. A consequence of this flipped binding mode is that the interactions between the hydroxyl and Asp267 and Glu219 are lost. However, the amines of inhibitor trans-(1S,2S)-AT and substrate cis-(1R,2S)-AT are both within methyl transfer distance of the cofactor. These results suggest that PNMT catalyzes transfer of methyl to ligand amines only when "anchor" interactions, such as those identified for the beta-hydroxyls of p-octopamine and cis-AT, are present.

  2. Detailed Analysis of the Binding Mode of Vanilloids to Transient Receptor Potential Vanilloid Type I (TRPV1) by a Mutational and Computational Study

    PubMed Central

    Mori, Yoshikazu; Ogawa, Kazuo; Warabi, Eiji; Yamamoto, Masahiro; Hirokawa, Takatsugu

    2016-01-01

    Transient receptor potential vanilloid type 1 (TRPV1) is a non-selective cation channel and a multimodal sensor protein. Since the precise structure of TRPV1 was obtained by electron cryo-microscopy, the binding mode of representative agonists such as capsaicin and resiniferatoxin (RTX) has been extensively characterized; however, detailed information on the binding mode of other vanilloids remains lacking. In this study, mutational analysis of human TRPV1 was performed, and four agonists (capsaicin, RTX, [6]-shogaol and [6]-gingerol) were used to identify amino acid residues involved in ligand binding and/or modulation of proton sensitivity. The detailed binding mode of each ligand was then simulated by computational analysis. As a result, three amino acids (L518, F591 and L670) were newly identified as being involved in ligand binding and/or modulation of proton sensitivity. In addition, in silico docking simulation and a subsequent mutational study suggested that [6]-gingerol might bind to and activate TRPV1 in a unique manner. These results provide novel insights into the binding mode of various vanilloids to the channel and will be helpful in developing a TRPV1 modulator. PMID:27606946

  3. Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.

    PubMed

    Chin, Ko-Hsin; Liang, Juin-Ming; Yang, Jauo-Guey; Shih, Min-Shao; Tu, Zhi-Le; Wang, Yu-Chuang; Sun, Xing-Han; Hu, Nien-Jen; Liang, Zhao-Xun; Dow, J Maxwell; Ryan, Robert P; Chou, Shan-Ho

    2015-08-11

    Cyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 Å. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-π interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-π, cation-π, backbone-π, or H2Olp-π interaction, but more commonly in the outer interaction zone by hydrophobic CH-π or π-π interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP.

  4. Identification of a novel selective PPARγ ligand with a unique binding mode and improved therapeutic profile in vitro

    PubMed Central

    Yi, Wei; Shi, Jingjing; Zhao, Guanguan; Zhou, X. Edward; Suino-Powell, Kelly; Melcher, Karsten; Xu, H. Eric

    2017-01-01

    Thiazolidinediones (TZD) function as potent anti-diabetic drugs through their direct action on the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), but their therapeutic benefits are compromised by severe side effects. To address this concern, here we developed a potent “hit” compound, VSP-51, which is a novel selective PPARγ-modulating ligand with improved therapeutic profiles in vitro compared to the multi-billion dollar TZD drug rosiglitazone (Rosi). Unlike Rosi, VSP-51 is a partial agonist of PPARγ with improved insulin sensitivity due to its ability to bind PPARγ with high affinity without stimulating adipocyte differentiation and the expression of adipogenesis-related genes. We have determined the crystal structure of the PPARγ ligand-binding domain (LBD) in complex with VSP-51, which revealed a unique mode of binding for VSP-51 and provides the molecular basis for the discrimination between VSP-51 from TZDs and other ligands such as telmisartan, SR1663 and SR1664. Taken together, our findings demonstrate that: a) VSP-51 can serve as a promising candidate for anti-diabetic drug discovery; and b) provide a rational basis for the development of future pharmacological agents targeting PPARγ with advantages over current TZD drugs. PMID:28128331

  5. Active site binding modes of inhibitors of Staphylococcus aureus mevalonate diphosphate decarboxylase from docking and molecular dynamics simulations.

    PubMed

    Addo, James K; Skaff, D Andrew; Miziorko, Henry M

    2016-01-01

    Bacterial mevalonate diphosphate decarboxylase (MDD) is an attractive therapeutic target for antibacterial drug development. In this work, we discuss a combined docking and molecular dynamics strategy toward inhibitor binding to bacterial MDD. The docking parameters utilized in this study were first validated with observations for the inhibitors 6-fluoromevalonate diphosphate (FMVAPP) and diphosphoglycolylproline (DPGP) using existing structures for the Staphylococcus epidermidis enzyme. The validated docking protocol was then used to predict structures of the inhibitors bound to Staphylococcus aureus MDD using the unliganded crystal structure of Staphylococcus aureus MDD. We also investigated a possible interactions improvement by combining this docking method with molecular dynamics simulations. Thus, the predicted docking structures were analyzed in a molecular dynamics trajectory to generate dynamic models and reinforce the predicted binding modes. FMVAPP is predicted to make more extensive contacts with S. aureus MDD, forming stable hydrogen bonds with Arg144, Arg193, Lys21, Ser107, and Tyr18, as well as making stable hydrophobic interactions with Tyr18, Trp19, and Met196. The differences in predicted binding are supported by experimentally determined Ki values of 0.23 ± 0.02 and 34 ± 8 μM, for FMVAPP and DPGP, respectively. The structural information coupled with the kinetic characterization obtained from this study should be useful in defining the requirements for inhibition as well as in guiding the selection of active compounds for inhibitor optimization.

  6. The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression

    PubMed Central

    Wu, Gang; Edmonson, Michael; Liu, Zhifa; Gruber, Tanja; Zhang, Jinghui; Pounds, Stan

    2014-01-01

    Summary: Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, we borrow ideas from the OASIS methods in the bioinformatics and statistics literature to develop the ‘most informative spacing test’ (MIST) for unsupervised detection of such transcriptomic features. In an example application involving 14 cases of pediatric acute megakaryoblastic leukemia, MIST more robustly identified features that perfectly discriminate subjects according to gender or the presence of a prognostically relevant fusion-gene than did seven other OASIS methods in the analysis of RNA-seq exon expression, RNA-seq exon junction expression and micorarray exon expression data. MIST was also effective at identifying features related to gender or molecular subtype in an example application involving 157 adult cases of acute myeloid leukemia. Availability: MIST will be freely available in the OASIS R package at http://www.stjuderesearch.org/site/depts/biostats Contact: stanley.pounds@stjude.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24458951

  7. Use of multiple acoustic wave modes for assessment of long bones: Model study

    PubMed Central

    Tatarinov, Alexey; Sarvazyan, Noune; Sarvazyan, Armen

    2010-01-01

    Multiple acoustic wave mode method has been proposed as a new modality in axial bone QUS. The new method is based on measurement of ultrasound velocity at different ratio of wavelength to the bone thickness, and taking into account both bulk and guided waves. It allows assessment of changes in both the material properties related to porosity and mineralization as well as the cortical thickness influenced by resorption from inner layers, which are equally important in diagnostics of osteoporosis and other bone osteopenia. Developed method was validated in model studies using a dual-frequency (100 and 500 kHz) ultrasound device. Three types of bone phantoms for long bones were developed and tested: (1) tubular specimens from polymer materials to model combined changes of material stiffness and cortical wall thickness; (2) layered specimens to model porosity in compact bone progressing from endosteum towards periosteum; (3) animal bone specimens with both cortical and trabecular components. Observed changes of the ultrasound velocity of guided waves at 100 kHz followed gradual changes in the thickness of the intact cortical layer. On the other hand, the bulk velocity at 500 kHz remained nearly constant at the different cortical layer thickness but was affected by the material stiffness. Similar trends were observed in phantoms and in fragments of animal bones. PMID:15982472

  8. Multiple secondary islands formation in nonlinear evolution of double tearing mode simulations

    NASA Astrophysics Data System (ADS)

    Guo, W.; Ma, J.; Yu, Z.

    2017-03-01

    A new numerical code solving the conservative perturbed resistive magnetohydrodynamic (MHD) model is developed. Numerical tests of the ideal Kelvin-Helmholtz instability and the resistive double tearing mode (DTM) show its capability in solving linear and nonlinear MHD instabilities. The nonlinear DTM evolution in 2D geometry is numerically investigated with low guiding field B z 0 , short half-distance y 0 between the equilibrium current sheets, and small resistivity η. The interaction of islands on the two initial current sheets may generate an unstable flow driven current sheet with a high length-to-thickness aspect ratio (α), and multiple secondary islands can form. In general, the length-to-thickness aspect ratio α and the number of secondary islands increase with decreasing guide field B z 0 , decreasing half-distance y 0 , and increasing Lundquist number of the flow driven current sheet S L although the dependence may be non-monotonic. The reconnection rate dependence on S L , B z 0 , and y 0 is also investigated.

  9. Low nanomolar GABA effects at extrasynaptic α4β1/β3δ GABA(A) receptor subtypes indicate a different binding mode for GABA at these receptors.

    PubMed

    Karim, Nasiara; Wellendorph, Petrine; Absalom, Nathan; Bang, Line Haunstrup; Jensen, Marianne Lerbech; Hansen, Maja Michelle; Lee, Ho Joon; Johnston, Graham A R; Hanrahan, Jane R; Chebib, Mary

    2012-08-15

    Ionotropic GABA(A) receptors are a highly heterogenous population of receptors assembled from a combination of multiple subunits. The aims of this study were to characterize the potency of GABA at human recombinant δ-containing extrasynaptic GABA(A) receptors expressed in Xenopus oocytes using the two-electrode voltage clamp technique, and to investigate, using site-directed mutagenesis, the molecular determinants for GABA potency at α4β3δ GABA(A) receptors. α4/δ-Containing GABA(A) receptors displayed high sensitivity to GABA, with mid-nanomolar concentrations activating α4β1δ (EC₅₀=24 nM) and α4β3δ (EC₅₀=12 nM) receptors. In the majority of oocytes expressing α4β3δ subtypes, GABA produced a biphasic concentration-response curve, and activated the receptor with low and high concentrations (EC₅₀(1)=16 nM; EC₅₀(2)=1.2 μM). At α4β2δ, GABA had low micromolar activity (EC₅₀=1 μM). An analysis of 10 N-terminal singly mutated α4β3δ receptors shows that GABA interacts with amino acids different to those reported for α1β2γ2 GABA(A) receptors. Residues Y205 and R207 of the β3-subunit significantly affected GABA potency, while the residue F71 of the α4- and the residue Y97 of the β3-subunit did not significantly affect GABA potency. Mutating the residue R218 of the δ-subunit, equivalent to the GABA binding residue R207 of the β2-subunit, reduced the potency of GABA by 670-fold, suggesting a novel GABA binding site at the δ-subunit interface. Taken together, GABA may have different binding modes for extrasynaptic δ-containing GABA(A) receptors compared to their synaptic counterparts.

  10. Diverse modes of binding in structures of Leishmania major N-myristoyltransferase with selective inhibitors

    PubMed Central

    Brannigan, James A.; Roberts, Shirley M.; Bell, Andrew S.; Hutton, Jennie A.; Hodgkinson, Michael R.; Tate, Edward W.; Leatherbarrow, Robin J.; Smith, Deborah F.; Wilkinson, Anthony J.

    2014-01-01

    The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT) has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed. PMID:25075346

  11. Structures of 5-Methylthioribose Kinase Reveal Substrate Specificity and Unusual Mode of Nucleotide Binding

    SciTech Connect

    Ku,S.; Yip, P.; Cornell, K.; Riscoe, M.; Behr, J.; Guillerm, G.; Howell, P.

    2007-01-01

    The methionine salvage pathway is ubiquitous in all organisms, but metabolic variations exist between bacteria and mammals. 5-Methylthioribose (MTR) kinase is a key enzyme in methionine salvage in bacteria and the absence of a mammalian homolog suggests that it is a good target for the design of novel antibiotics. The structures of the apo-form of Bacillus subtilis MTR kinase, as well as its ADP, ADP-PO4, AMPPCP, and AMPPCP-MTR complexes have been determined. MTR kinase has a bilobal eukaryotic protein kinase fold but exhibits a number of unique features. The protein lacks the DFG motif typically found at the beginning of the activation loop and instead coordinates magnesium via a DXE motif (Asp{sup 250}-Glu{sup 252}). In addition, the glycine-rich loop of the protein, analogous to the 'Gly triad' in protein kinases, does not interact extensively with the nucleotide. The MTR substrate-binding site consists of Asp{sup 233} of the catalytic HGD motif, a novel twin arginine motif (Arg{sup 340}/Arg{sup 341}), and a semi-conserved W-loop, which appears to regulate MTR binding specificity. No lobe closure is observed for MTR kinase upon substrate binding. This is probably because the enzyme lacks the lobe closure/inducing interactions between the C-lobe of the protein and the ribosyl moiety of the nucleotide that are typically responsible for lobe closure in protein kinases. The current structures suggest that MTR kinase has a dissociative mechanism.

  12. Despite a Conserved Cystine Knot Motif, Different Cyclotides Have Different Membrane Binding Modes

    PubMed Central

    Wang, Conan K.; Colgrave, Michelle L.; Ireland, David C.; Kaas, Quentin; Craik, David J.

    2009-01-01

    Abstract Cyclotides are cyclic proteins produced by plants for defense against pests. Because of their remarkable stability and diverse bioactivities, they have a range of potential therapeutic applications. The bioactivities of cyclotides are believed to be mediated through membrane interactions. To determine the structural basis for the biological activity of the two major subfamilies of cyclotides, we determined the conformation and orientation of kalata B2 (kB2), a Möbius cyclotide, and cycloviolacin O2 (cO2), a bracelet cyclotide, bound to dodecylphosphocholine micelles, using NMR spectroscopy in the presence and absence of 5- and 16-doxylstearate relaxation probes. Analysis of binding curves using the Langmuir isotherm indicated that cO2 and kB2 have association constants of 7.0 × 103 M−1 and 6.0 × 103 M−1, respectively, consistent with the notion that they are bound near the surface, rather than buried deeply within the micelle. This suggestion is supported by the selective broadening of micelle-bound cyclotide NMR signals upon addition of paramagnetic Mn ions. The cyclotides from the different subfamilies exhibited clearly different binding orientations at the micelle surface. Structural analysis of cO2 confirmed that the main element of the secondary structure is a β-hairpin centered in loop 5. A small helical turn is present in loop 3. Analysis of the surface profile of cO2 shows that a hydrophobic patch stretches over loops 2 and 3, in contrast to the hydrophobic patch of kB2, which predominantly involves loops 2 and 5. The different location of the hydrophobic patches in the two cyclotides explains their different binding orientations and provides an insight into the biological activities of cyclotides. PMID:19720036

  13. Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode.

    PubMed Central

    Blankenfeldt, W.; Nowicki, C.; Montemartini-Kalisz, M.; Kalisz, H. M.; Hecht, H. J.

    1999-01-01

    The crystal structure of tyrosine aminotransferase (TAT) from the parasitic protozoan Trypanosoma cruzi, which belongs to the aminotransferase subfamily Igamma, has been determined at 2.5 A resolution with the R-value R = 15.1%. T. cruzi TAT shares less than 15% sequence identity with aminotransferases of subfamily Ialpha but shows only two larger topological differences to the aspartate aminotransferases (AspATs). First, TAT contains a loop protruding from the enzyme surface in the larger cofactor-binding domain, where the AspATs have a kinked alpha-helix. Second, in the smaller substrate-binding domain, TAT has a four-stranded antiparallel beta-sheet instead of the two-stranded beta-sheet in the AspATs. The position of the aromatic ring of the pyridoxal-5'-phosphate cofactor is very similar to the AspATs but the phosphate group, in contrast, is closer to the substrate-binding site with one of its oxygen atoms pointing toward the substrate. Differences in substrate specificities of T. cruzi TAT and subfamily Ialpha aminotransferases can be attributed by modeling of substrate complexes mainly to this different position of the cofactor-phosphate group. Absence of the arginine, which in the AspATs fixes the substrate side-chain carboxylate group by a salt bridge, contributes to the inability of T. cruzi TAT to transaminate acidic amino acids. The preference of TAT for tyrosine is probably related to the ability of Asn17 in TAT to form a hydrogen bond to the tyrosine side-chain hydroxyl group. PMID:10595543

  14. Teaching Multiple Modes of Representation in Middle-School Science Classrooms: Impact on Student Learning and Multimodal Use

    ERIC Educational Resources Information Center

    Nixon, Ryan S.; Smith, Leigh K.; Wimmer, Jennifer J.

    2015-01-01

    This quasi-experimental study investigated how explicit instruction about multiple modes of representation (MMR) impacted grades 7 (n = 61) and 8 (n = 141) students' learning and multimodal use on end-of-unit assessments. Half of each teacher's (n = 3) students received an intervention consisting of explicit instruction on MMR in science…

  15. Multiple sup 3 H-oxytocin binding sites in rat myometrial plasma membranes

    SciTech Connect

    Crankshaw, D.; Gaspar, V.; Pliska, V. )

    1990-01-01

    The affinity spectrum method has been used to analyse binding isotherms for {sup 3}H-oxytocin to rat myometrial plasma membranes. Three populations of binding sites with dissociation constants (Kd) of 0.6-1.5 x 10(-9), 0.4-1.0 x 10(-7) and 7 x 10(-6) mol/l were identified and their existence verified by cluster analysis based on similarities between Kd, binding capacity and Hill coefficient. When experimental values were compared to theoretical curves constructed using the estimated binding parameters, good fits were obtained. Binding parameters obtained by this method were not influenced by the presence of GTP gamma S (guanosine-5'-O-3-thiotriphosphate) in the incubation medium. The binding parameters agree reasonably well with those found in uterine cells, they support the existence of a medium affinity site and may allow for an explanation of some of the discrepancies between binding and response in this system.

  16. Multiple-bunch-length operating mode design for a storage ring using hybrid low alpha and harmonic cavity method

    NASA Astrophysics Data System (ADS)

    Gao, Weiwei; Wang, Lin; Li, Heting

    2017-03-01

    In this paper we design a simultaneous three bunch length operating mode at the HLS-II (Hefei Light Source II) storage ring by installing two harmonic cavities and minimizing the momentum compaction factor. The short bunches (2.6 mm) presented in this work will meet the requirement of coherent millimeter-wave and sub-THz radiation experiments, while the long bunches (20 mm) will efficiently increase the total beam current. Therefore, this multiple-bunch-length operating mode allows present synchrotron users and coherent millimeter-wave users (or sub THz users) to carry out their experiments simultaneously. Since the relatively low energy characteristic of HLS-II we achieve the multiple-bunch-length operating mode without multicell superconducting RF cavities, which is technically feasible.

  17. In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study.

    PubMed

    Gadhe, Changdev G; Balupuri, Anand; Cho, Seung Joo

    2015-01-01

    Human CC-chemokine receptor 8 (CCR8) is a crucial drug target in asthma that belongs to G-protein-coupled receptor superfamily, which is characterized by seven transmembrane helices. To date, there is no X-ray crystal structure available for CCR8; this hampers active research on the target. Molecular basis of interaction mechanism of antagonist with CCR8 remains unclear. In order to provide binding site information and stable binding mode, we performed modeling, docking and molecular dynamics (MD) simulation of CCR8. Docking study of biaryl-ether-piperidine derivative (13C) was performed inside predefined CCR8 binding site to get the representative conformation of 13C. Further, MD simulations of receptor and complex (13C-CCR8) inside dipalmitoylphosphatidylcholine lipid bilayers were performed to explore the effect of lipids. Results analyses showed that the Gln91, Tyr94, Cys106, Val109, Tyr113, Cys183, Tyr184, Ser185, Lys195, Thr198, Asn199, Met202, Phe254, and Glu286 were conserved in both docking and MD simulations. This indicated possible role of these residues in CCR8 antagonism. However, experimental mutational studies on these identified residues could be effective to confirm their importance in CCR8 antagonism. Furthermore, calculated Coulombic interactions represented the crucial roles of Glu286, Lys195, and Tyr113 in CCR8 antagonism. Important residues identified in this study overlap with the previous non-peptide agonist (LMD-009) binding site. Though, the non-peptide agonist and currently studied inhibitor (13C) share common substructure, but they differ in their effects on CCR8. So, to get more insight into their agonist and antagonist effects, further side-by-side experimental studies on both agonist (LMD-009) and antagonist (13C) are suggested.

  18. Modeling androgen receptor flexibility: a binding mode hypothesis of CYP17 inhibitors/antiandrogens for prostate cancer therapy.

    PubMed

    Gianti, Eleonora; Zauhar, Randy J

    2012-10-22

    Prostate Cancer (PCa), a leading cause of cancer death worldwide (www.cancer.gov), is a complex malignancy where a spectrum of targets leads to a diversity of PCa forms. A widely pursued therapeutic target is the Androgen Receptor (AR). As a Steroid Hormone Receptor, AR serves as activator of transcription upon binding to androgens and plays a central role in the development of PCa. AR is a structurally flexible protein, and conformational plasticity of residues in the binding-pocket is a key to its ability to accommodate ligands from various chemical classes. Besides direct modulation of AR activity by antagonists, inhibition of cytochrome CYP17 (17α-hydroxylase/17,20-lyase), essential in androgen biosynthesis, has widely been considered an effective strategy against PCa. Interestingly, Handratta et al. (2005) discovered new, potent inhibitors of CYP17 (C-17 steroid derivatives) with pure AR antagonistic properties. Although the antiandrogenic activity of their lead compound (VN/124-1) has been experimentally proven both in vitro and in vivo, no structural data are currently available to elucidate the molecular determinants responsible for these desirable dual inhibitory properties. We implemented a Structure-based Drug Design (SBDD) approach to generate a valuable hypothesis as to the binding modes of steroidal CYP17 inhibitors/antiandrogens against the AR. To deal with the plasticity of residues buried in the Ligand Binding Domain (LBD), we developed a flexible-receptor Docking protocol based on Induced-Fit (IFD) methodology (www.schrodinger.com/). Our results constitute an ideal starting point for the rational design of next-generation analogues of CYP17 inhibitors/antiandrogens as well as an attractive tool to suggest novel chemical classes of AR antagonists.

  19. Salmonella Enterica Serovar Typhimurium BipA Exhibits Two Distinct Ribosome Binding Modes

    SciTech Connect

    deLivron, M.; Robinson, V

    2008-01-01

    BipA is a highly conserved prokaryotic GTPase that functions to influence numerous cellular processes in bacteria. In Escherichia coli and Salmonella enterica serovar Typhimurium, BipA has been implicated in controlling bacterial motility, modulating attachment and effacement processes, and upregulating the expression of virulence genes and is also responsible for avoidance of host defense mechanisms. In addition, BipA is thought to be involved in bacterial stress responses, such as those associated with virulence, temperature, and symbiosis. Thus, BipA is necessary for securing bacterial survival and successful invasion of the host. Steady-state kinetic analysis and pelleting assays were used to assess the GTPase and ribosome-binding properties of S. enterica BipA. Under normal bacterial growth, BipA associates with the ribosome in the GTP-bound state. However, using sucrose density gradients, we demonstrate that the association of BipA and the ribosome is altered under stress conditions in bacteria similar to those experienced during virulence. The data show that this differential binding is brought about by the presence of ppGpp, an alarmone that signals the onset of stress-related events in bacteria.

  20. Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.

    PubMed

    Gregg, Katie J; Finn, Ron; Abbott, D Wade; Boraston, Alisdair B

    2008-05-02

    The genomes of myonecrotic Clostridium perfringens isolates contain genes encoding a large and fascinating array of highly modular glycoside hydrolase enzymes. Although the catalytic activities of many of these enzymes are somewhat predictable based on their amino acid sequences, the functions of their abundant ancillary modules are not and remain poorly studied. Here, we present the structural and functional analysis of a new family of ancillary carbohydrate-binding modules (CBMs), CBM51, which was previously annotated in data bases as the novel putative CBM domain. The high resolution crystal structures of two CBM51 members, GH95CBM51 and GH98CBM51, from a putative family 95 alpha-fucosidase and from a family 98 blood group A/B antigen-specific endo-beta-galactosidase, respectively, showed them to have highly similar beta-sandwich folds. However, GH95CBM51 was shown by glycan microarray screening, isothermal titration calorimetry, and x-ray crystallography to bind galactose residues, whereas the same analyses of GH98CBM51 revealed specificity for the blood group A/B antigens through non-conserved interactions. Overall, this work identifies a new family of CBMs with many members having apparent specificity for eukaryotic glycans, in keeping with the glycan-rich environment C. perfringens would experience in its host. However, a wider bioinformatic analysis of this CBM family also indicated a large number of members in non-pathogenic environmental bacteria, suggesting a role in the recognition of environmental glycans.

  1. The pKa of butaclamol and the mode of butaclamol binding to central dopamine receptors.

    PubMed

    Chrzanowski, F A; McGrogan, B A; Maryanoff, B E

    1985-03-01

    The pKa values for butaclamol (1), 1,2,3,5,6,10b beta-hexahydro-6 alpha-phenylpyrrolo[2,1-alpha]isoquinoline (2, McN-4612-Y), and 2-tert-butyl-1,3,4,6,7,11b beta-hexahydro-7 beta-phenyl-2H-benzo[alpha]quinolizin-2 alpha-ol (3, McN-4171) were determined to be 7.2, 9.1, and 7.0, respectively. The values for 1 and 3 are anomalous; however, the value for 1 (7.2) is not as low as the one reported in the literature (pKa = 5.9). We also determined pKa values for apomorphine, chlorpromazine, and lidocaine, for reference purposes (7.6, 9.2, and 7.9, respectively). The results indicate that 1 would not be predominantly unprotonated under the physiological conditions of receptor binding, rather it would be about 50% protonated. This fact may contravene a suggested binding model used to map the central dopamine receptor (viz., ref 3).

  2. TAF4/4b·TAF12 Displays a Unique Mode of DNA Binding and Is Required for Core Promoter Function of a Subset of Genes*

    PubMed Central

    Gazit, Kfir; Moshonov, Sandra; Elfakess, Rofa; Sharon, Michal; Mengus, Gabrielle; Davidson, Irwin; Dikstein, Rivka

    2009-01-01

    The major core promoter-binding factor in polymerase II transcription machinery is TFIID, a complex consisting of TBP, the TATA box-binding protein, and 13 to 14 TBP-associated factors (TAFs). Previously we found that the histone H2A-like TAF paralogs TAF4 and TAF4b possess DNA-binding activity. Whether TAF4/TAF4b DNA binding directs TFIID to a specific core promoter element or facilitates TFIID binding to established core promoter elements is not known. Here we analyzed the mode of TAF4b·TAF12 DNA binding and show that this complex binds DNA with high affinity. The DNA length required for optimal binding is ∼70 bp. Although the complex displays a weak sequence preference, the nucleotide composition is less important than the length of the DNA for high affinity binding. Comparative expression profiling of wild-type and a DNA-binding mutant of TAF4 revealed common core promoter features in the down-regulated genes that include a TATA-box and an Initiator. Further examination of the PEL98 gene from this group showed diminished Initiator activity and TFIID occupancy in TAF4 DNA-binding mutant cells. These findings suggest that DNA binding by TAF4/4b-TAF12 facilitates the association of TFIID with the core promoter of a subset of genes. PMID:19635797

  3. Sensitive determination of plasma protein binding of cationic drugs using mixed-mode solid-phase microextraction.

    PubMed

    Peltenburg, Hester; Bosman, Ingrid J; Hermens, Joop L M

    2015-11-10

    Freely dissolved concentrations are considered to be the most relevant concentration in pharmacology and toxicology, as they represent the active concentration available for interaction with its surroundings. Here, a solid-phase microextraction (SPME) coating that combines octadecyl and propylsulfonic acid groups as strong cation exchange sites, known as C18/SCX or "mixed-mode" SPME, is used to measure freely dissolved concentrations of amitriptyline, amphetamine, diazepam and tramadol to different binding matrices, including bovine serum albumin (BSA), human serum albumin (HSA), human plasma and human whole blood. A potential confounding factor in binding studies is that proteins may sorb to the fiber coating leading to incorrect measurement of protein sorption or changes in uptake kinetics to the fiber coating. Sorption of bovine serum albumin (BSA) was observed and quantified using a Lowry assay. BSA binds to the C18/SCX fiber in small amounts, but large changes in uptake kinetics were not observed. All experiments were performed at equilibrium. In addition, however, the effect of depletion and non-equilibrium extraction on the estimation of protein binding affinities was also studied. Binding affinities to BSA and human serum albumin (HSA) were calculated as log KBSA or log KHSA. These values were very similar to reported literature values. Sampling at either equilibrium or non-equilibrium resulted in similar binding affinities. Furthermore, SPME fibers were used to measure freely dissolved concentrations in undiluted human plasma and whole blood. Analysis of SPME extracts could be performed using HPLC-UV or HPLC with fluorescence detection without prior clean-up of the samples. Measured bound fractions in plasma using this SPME approach were comparable to literature reference values. Bound fractions in whole blood were always higher than in plasma, due to red blood cell partitioning. This work shows the potential of SPME as sampling tool for freely dissolved

  4. Mode of Action of the Polyene Antibiotic Candicidin: Binding Factors in the Wall of Candida albicans

    PubMed Central

    Hammond, S. M.; Kliger, B. N.

    1976-01-01

    The polyene antibiotic candicidin produces a rapid efflux of K+ ions from a suspension of Candida albicans. Onset of K+ leakage depends on the culture age, stationary-phase yeasts leaking K+ more slowly than exponential-phase yeasts. The time taken for potassium leakage to begin represents the time taken by the antibiotic to cross the cell wall and produce membrane damage. It was shown that there were factors in the cell wall of C. albicans that increased their total binding capacity and their affinity for candicidin during growth. An attempt was made to relate changes in the lipid content of the yeast cell with the increased time taken to produce membrane damage. PMID:773298

  5. Diverse binding modes, same goal: the receptor recognition mechanism of botulinum neurotoxin

    PubMed Central

    Lam, Kwok-Ho; Yao, Guorui; Jin, Rongsheng

    2015-01-01

    Botulinum neurotoxins (BoNTs) are among the most deadly toxins known. They act rapidly in a highly specific manner to block neurotransmitter release by cleaving the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) complex at neuromuscular junctions. The extreme toxicity of BoNTs relies predominantly on their neurotropism that is accomplished by recognition of two host receptors, a polysialo-ganglioside and in the majority of cases a synaptic vesicle protein, through their receptor-binding domains. Two proteins, synaptotagmin and synaptic vesicle glycoprotein 2, have been identified as the receptors for various serotypes of BoNTs. Here, we review recent breakthroughs in the structural studies of BoNT–protein receptor recognitions that highlight a range of diverse mechanisms by which BoNTs manipulate host neuronal proteins for highly specific uptake at neuromuscular junctions. PMID:25701633

  6. A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism

    PubMed Central

    Eyal, Zohar; Matzov, Donna; Krupkin, Miri; Paukner, Susanne; Riedl, Rosemarie; Rozenberg, Haim; Zimmerman, Ella; Bashan, Anat; Yonath, Ada

    2016-01-01

    The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug’s selectivity. PMID:27958389

  7. Multiple specific binding sites for purified glucocorticoid receptors on mammary tumor virus DNA.

    PubMed

    Payvar, F; Firestone, G L; Ross, S R; Chandler, V L; Wrange, O; Carlstedt-Duke, J; Gustafsson, J A; Yamamoto, K R

    1982-01-01

    Glucocorticoid hormones selectively stimulate the rate of transcription of integrated mammary tumor virus (MTV) sequences in infected rat hepatoma cells. Using two independent assays, we find that purified rat liver glucocorticoid receptor protein binds specifically to at least four widely separated regions on pure MTV proviral DNA. One of these specific binding domains, which itself contains at least two distinct receptor binding sites, resides within a fragment of viral DNA that maps 110-449 bp upstream of the promoter for MTV RNA synthesis. Three other binding domains lie downstream of the promoter and within the MTV primary transcription unit. Restriction fragments bearing separate binding domains have been introduced into cultured cells; transformants have been recovered in which the introduced fragments are expressed under glucocorticoid control. Thus, it appears that this assay will be useful for assessing the biological significance of the receptor binding sites detected in vitro.

  8. Thermodynamics and binding mode of novel structurally related 1,2,4-thiadiazole derivatives with native and modified cyclodextrins

    NASA Astrophysics Data System (ADS)

    Terekhova, Irina V.; Chislov, Mikhail V.; Brusnikina, Maria A.; Chibunova, Ekaterina S.; Volkova, Tatyana V.; Zvereva, Irina A.; Proshin, Alexey N.

    2017-03-01

    Study of complex formation of cyclodextrins with 1,2,4-thiadiazole derivatives intended for Alzheimer's disease treatment was carried out using 1H NMR, ITC and phase solubility methods. Structure of cyclodextrins and thiadiazoles affects the binding mode and thermodynamics of complexation. The larger cavity of β- and γ-cyclodextrins is more appropriate for deeper insertion of 1,2,4-thiadiazole derivatives which is accompanied by intensive dehydration and solvent reorganization. Benzene ring of the thiadiazoles is located inside macrocyclic cavity while piperidine ring is placed outside the cavity and can form H-bonds with cyclodextrin exterior. Complexation with cyclodextrins induces the enhancement of aqueous solubility of 1,2,4-thiadiazole derivatives.

  9. Use of multiple modes of flight subsidy by a soaring terrestrial bird, the golden eagle Aquila chrysaetos, when on migration

    PubMed Central

    Katzner, Todd E.; Turk, Philip J.; Duerr, Adam E.; Miller, Tricia A.; Lanzone, Michael J.; Cooper, Jeff L.; Brandes, David; Tremblay, Junior A.; Lemaître, Jérôme

    2015-01-01

    Large birds regularly use updrafts to subsidize flight. Although most research on soaring bird flight has focused on use of thermal updrafts, there is evidence suggesting that many species are likely to use multiple modes of subsidy. We tested the degree to which a large soaring species uses multiple modes of subsidy to provide insights into the decision-making that underlies flight behaviour. We statistically classified more than 22 000 global positioning satellite–global system for mobile communications telemetry points collected at 30-s intervals to identify the type of subsidized flight used by 32 migrating golden eagles during spring in eastern North America. Eagles used subsidized flight on 87% of their journey. They spent 41.9% ± 1.5 (, range: 18–56%) of their subsidized northbound migration using thermal soaring, 45.2% ± 2.1 (12–65%) of time gliding between thermals, and 12.9% ± 2.2 (1–55%) of time using orographic updrafts. Golden eagles responded to the variable local-scale meteorological events they encountered by switching flight behaviour to take advantage of multiple modes of subsidy. Orographic soaring occurred more frequently in morning and evening, earlier in the migration season, and when crosswinds and tail winds were greatest. Switching between flight modes allowed migration for relatively longer periods each day and frequent switching behaviour has implications for a better understanding of avian flight behaviour and of the evolution of use of subsidy in flight. PMID:26538556

  10. Use of multiple modes of flight subsidy by a soaring terrestrial bird, the golden eagle Aquila chrysaetos, when on migration.

    PubMed

    Katzner, Todd E; Turk, Philip J; Duerr, Adam E; Miller, Tricia A; Lanzone, Michael J; Cooper, Jeff L; Brandes, David; Tremblay, Junior A; Lemaître, Jérôme

    2015-11-06

    Large birds regularly use updrafts to subsidize flight. Although most research on soaring bird flight has focused on use of thermal updrafts, there is evidence suggesting that many species are likely to use multiple modes of subsidy. We tested the degree to which a large soaring species uses multiple modes of subsidy to provide insights into the decision-making that underlies flight behaviour. We statistically classified more than 22 000 global positioning satellite-global system for mobile communications telemetry points collected at 30-s intervals to identify the type of subsidized flight used by 32 migrating golden eagles during spring in eastern North America. Eagles used subsidized flight on 87% of their journey. They spent 41.9% ± 1.5 ([Formula: see text], range: 18-56%) of their subsidized northbound migration using thermal soaring, 45.2% ± 2.1 (12-65%) of time gliding between thermals, and 12.9% ± 2.2 (1-55%) of time using orographic updrafts. Golden eagles responded to the variable local-scale meteorological events they encountered by switching flight behaviour to take advantage of multiple modes of subsidy. Orographic soaring occurred more frequently in morning and evening, earlier in the migration season, and when crosswinds and tail winds were greatest. Switching between flight modes allowed migration for relatively longer periods each day and frequent switching behaviour has implications for a better understanding of avian flight behaviour and of the evolution of use of subsidy in flight.

  11. Binding Mode of CpG Oligodeoxynucleotides to Nanoparticles Regulates Bifurcated Cytokine induction via Toll-like Receptor 9

    PubMed Central

    Chinnathambi, Shanmugavel; Chen, Song; Ganesan, Singaravelu; Hanagata, Nobutaka

    2012-01-01

    The interaction of cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs) with Toll-like receptor 9 (TLR9) activates the immune system. Multimeric class A CpG ODNs induce interferon-α (IFN-α) and, to a lesser extent, interleukin-6. By contrast, monomeric class B CpG ODNs induce interleukin-6 but not IFN-α. This difference suggests that the multimerization of CpG ODN molecules is a key factor in IFN-α induction. We multimerized class B CpG ODN2006x3-PD molecules that consist entirely of a phosphodiester backbone onto quantum dot silicon nanoparticles with various binding modes. Herein, we present the binding mode–dependent bifurcation of cytokine induction and discuss its possible mechanism of CpG ODN and TLR9 interaction. Our discoveries also suggest that nanoparticles play roles in not only delivery of CpG ODNs but also control of CpG ODN activity. PMID:22837814

  12. Binding mode of triazole derivatives as aromatase inhibitors based on docking, protein ligand interaction fingerprinting, and molecular dynamics simulation studies

    PubMed Central

    Mojaddami, Ayyub; Sakhteman, Amirhossein; Fereidoonnezhad, Masood; Faghih, Zeinab; Najdian, Atena; Khabnadideh, Soghra; Sadeghpour, Hossein; Rezaei, Zahra

    2017-01-01

    Aromatase inhibitors (AIs) as effective candidates have been used in the treatment of hormone-dependent breast cancer. In this study, we have proposed 300 structures as potential AIs and filtered them by Lipinski's rule of five using DrugLito software. Subsequently, they were subjected to docking simulation studies to select the top 20 compounds based on their Gibbs free energy changes and also to perform more studies on the protein-ligand interaction fingerprint by AuposSOM software. In this stage, anastrozole and letrozole were used as positive control to compare their interaction fingerprint patterns with our proposed structures. Finally, based on the binding energy values, one active structure (ligand 15) was selected for molecular dynamic simulation in order to get information for the binding mode of these ligands within the enzyme cavity. The triazole of ligand 15 pointed to HEM group in aromatase active site and coordinated to Fe of HEM through its N4 atom. In addition, two π-cation interactions was also observed, one interaction between triazole and porphyrin of HEM group, and the other was 4-chloro phenyl moiety of this ligand with Arg115 residue. PMID:28255310

  13. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification

    PubMed Central

    Fang, Pengfei; Guo, Min

    2015-01-01

    Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories. PMID:26670257

  14. A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks.

    PubMed

    Huang, Hongda; Strømme, Caroline B; Saredi, Giulia; Hödl, Martina; Strandsby, Anne; González-Aguilera, Cristina; Chen, Shoudeng; Groth, Anja; Patel, Dinshaw J

    2015-08-01

    During DNA replication, chromatin is reassembled by recycling of modified old histones and deposition of new ones. How histone dynamics integrates with DNA replication to maintain genome and epigenome information remains unclear. Here, we reveal how human MCM2, part of the replicative helicase, chaperones histones H3-H4. Our first structure shows an H3-H4 tetramer bound by two MCM2 histone-binding domains (HBDs), which hijack interaction sites used by nucleosomal DNA. Our second structure reveals MCM2 and ASF1 cochaperoning an H3-H4 dimer. Mutational analyses show that the MCM2 HBD is required for MCM2-7 histone-chaperone function and normal cell proliferation. Further, we show that MCM2 can chaperone both new and old canonical histones H3-H4 as well as H3.3 and CENPA variants. The unique histone-binding mode of MCM2 thus endows the replicative helicase with ideal properties for recycling histones genome wide during DNA replication.

  15. Development of Small-Molecule Trypanosoma brucei N-Myristoyltransferase Inhibitors: Discovery and Optimisation of a Novel Binding Mode

    PubMed Central

    Spinks, Daniel; Smith, Victoria; Thompson, Stephen; Robinson, David A; Luksch, Torsten; Smith, Alasdair; Torrie, Leah S; McElroy, Stuart; Stojanovski, Laste; Norval, Suzanne; Collie, Iain T; Hallyburton, Irene; Rao, Bhavya; Brand, Stephen; Brenk, Ruth; Frearson, Julie A; Read, Kevin D; Wyatt, Paul G; Gilbert, Ian H

    2015-01-01

    The enzyme N-myristoyltransferase (NMT) from Trypanosoma brucei has been validated both chemically and biologically as a potential drug target for human African trypanosomiasis. We previously reported the development of some very potent compounds based around a pyrazole sulfonamide series, derived from a high-throughput screen. Herein we describe work around thiazolidinone and benzomorpholine scaffolds that were also identified in the screen. An X-ray crystal structure of the thiazolidinone hit in Leishmania major NMT showed the compound bound in the previously reported active site, utilising a novel binding mode. This provides potential for further optimisation. The benzomorpholinone was also found to bind in a similar region. Using an X-ray crystallography/structure-based design approach, the benzomorpholinone series was further optimised, increasing activity against T. brucei NMT by >1000-fold. A series of trypanocidal compounds were identified with suitable in vitro DMPK properties, including CNS exposure for further development. Further work is required to increase selectivity over the human NMT isoform and activity against T. brucei. PMID:26395087

  16. A designed inhibitor of a CLC antiporter blocks function through a unique binding mode

    PubMed Central

    Howery, Andrew E.; Elvington, Shelley; Abraham, Sherwin J.; Choi, Kee-Hyun; Phillips, Sabrina; Ryan, Christopher M.; Sanford, R. Lea; Simpson-Dworschak, Sierra; Almqvist, Jonas; Tran, Kevin; Chew, Thomas A.; Zachariae, Ulrich; Andersen, Olaf S.; Whitelegge, Julian; Matulef, Kimberly; Du Bois, Justin; Maduke, Merritt C.

    2012-01-01

    SUMMARY The lack of small-molecule inhibitors for anion-selective transporters and channels has impeded our understanding of the complex mechanisms that underlie ion passage. The ubiquitous CLC “Chloride Channel” family represents a unique target for biophysical and biochemical studies because its distinctive protein fold supports both passive chloride channels and secondary-active chloride-proton transporters. Here, we describe the synthesis and characterization of the first specific small-molecule inhibitor directed against a CLC antiporter (ClC-ec1). This compound, 4,4′-octanamidostilbene-2,2′-disulfonate (OADS), inhibits ClC-ec1 with low micromolar affinity and has no specific effect on a CLC channel (ClC-1). Inhibition of ClC-ec1 occurs by binding to two distinct intracellular sites. The location of these sites and the lipid-dependence of inhibition suggest potential mechanisms of action. The discovery of this compound will empower research to elucidate differences between antiporter and channel mechanisms and to develop treatments for CLC-mediated disorders. PMID:23177200

  17. Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B

    PubMed Central

    Jin, Tiantian; Yu, Haibo; Huang, Xu-Feng

    2016-01-01

    Protein Tyrosine Phosphatase 1B (PTP1B) has been recognized as a promising therapeutic target for treating obesity, diabetes, and certain cancers for over a decade. Previous drug design has focused on inhibitors targeting the active site of PTP1B. However, this has not been successful because the active site is positively charged and conserved among the protein tyrosine phosphatases. Therefore, it is important to develop PTP1B inhibitors with alternative inhibitory strategies. Using computational studies including molecular docking, molecular dynamics simulations, and binding free energy calculations, we found that lupane triterpenes selectively inhibited PTP1B by targeting its more hydrophobic and less conserved allosteric site. These findings were verified using two enzymatic assays. Furthermore, the cell culture studies showed that lupeol and betulinic acid inhibited the PTP1B activity stimulated by TNFα in neurons. Our study indicates that lupane triterpenes are selective PTP1B allosteric inhibitors with significant potential for treating those diseases with elevated PTP1B activity. PMID:26865097

  18. Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex.

    PubMed

    Blosser, Timothy R; Loeff, Luuk; Westra, Edze R; Vlot, Marnix; Künne, Tim; Sobota, Małgorzata; Dekker, Cees; Brouns, Stan J J; Joo, Chirlmin

    2015-04-02

    Small RNA-guided protein complexes play an essential role in CRISPR-mediated immunity in prokaryotes. While these complexes initiate interference by flagging cognate invader DNA for destruction, recent evidence has implicated their involvement in new CRISPR memory formation, called priming, against mutated invader sequences. The mechanism by which the target recognition complex mediates these disparate responses-interference and priming-remains poorly understood. Using single-molecule FRET, we visualize how bona fide and mutated targets are differentially probed by E. coli Cascade. We observe that the recognition of bona fide targets is an ordered process that is tightly controlled for high fidelity. Mutated targets are recognized with low fidelity, which is featured by short-lived and PAM- and seed-independent binding by any segment of the crRNA. These dual roles of Cascade in immunity with distinct fidelities underpin CRISPR-Cas robustness, allowing for efficient degradation of bona fide targets and priming of mutated DNA targets.

  19. A designed inhibitor of a CLC antiporter blocks function through a unique binding mode.

    PubMed

    Howery, Andrew E; Elvington, Shelley; Abraham, Sherwin J; Choi, Kee-Hyun; Dworschak-Simpson, Sierra; Phillips, Sabrina; Ryan, Christopher M; Sanford, R Lea; Almqvist, Jonas; Tran, Kevin; Chew, Thomas A; Zachariae, Ulrich; Andersen, Olaf S; Whitelegge, Julian; Matulef, Kimberly; Du Bois, Justin; Maduke, Merritt C

    2012-11-21

    The lack of small-molecule inhibitors for anion-selective transporters and channels has impeded our understanding of the complex mechanisms that underlie ion passage. The ubiquitous CLC "Chloride Channel" family represents a unique target for biophysical and biochemical studies because its distinctive protein fold supports both passive chloride channels and secondary-active chloride-proton transporters. Here, we describe the synthesis and characterization of a specific small-molecule inhibitor directed against a CLC antiporter (ClC-ec1). This compound, 4,4'-octanamidostilbene-2,2'-disulfonate (OADS), inhibits ClC-ec1 with low micromolar affinity and has no specific effect on a CLC channel (ClC-1). Inhibition of ClC-ec1 occurs by binding to two distinct intracellular sites. The location of these sites and the lipid dependence of inhibition suggest potential mechanisms of action. This compound will empower research to elucidate differences between antiporter and channel mechanisms and to develop treatments for CLC-mediated disorders.

  20. Homology modeling of Homo sapiens Lipoic acid Synthase: substrate docking and insights on its binding mode.

    PubMed

    Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

    2016-10-04

    Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X - ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS - SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein.

  1. Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains

    PubMed Central

    Liu, Junfeng; Huang, Jinguang; Zhao, Yanxiang; Liu, Huaian; Wang, Dawei; Yang, Jun; Zhao, Wensheng; Taylor, Ian A.; Peng, You-Liang

    2015-01-01

    The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB–DNA. The structure revealed that the wing, the 20-loop, helix A and helix B in PCG2–DBD are important elements for DNA binding. Unlike previously characterized wHTH proteins, PCG2–DBD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB–DNA whilst the 20-loop and helix A interact non-specifically with DNA. Notably, two glutamines Q89 and Q82 within the wing were found to recognize the MCB core CGCG sequence through making hydrogen bond interactions. Further in vitro assays confirmed essential roles of Q89 and Q82 in the DNA binding. These data together indicate that the MBP1 homologue PCG2 employs an unusual mode of binding to target DNA and demonstrate the versatility of wHTH domains. PMID:25550425

  2. Binding mode analyses and pharmacophore model development for stilbene derivatives as a novel and competitive class of α-glucosidase inhibitors.

    PubMed

    Lee, Yuno; Kim, Songmi; Kim, Jun Young; Arooj, Mahreen; Kim, Siu; Hwang, Swan; Kim, Byeong-Woo; Park, Ki Hun; Lee, Keun Woo

    2014-01-01

    Stilbene urea derivatives as a novel and competitive class of non-glycosidic α-glucosidase inhibitors are effective for the treatment of type II diabetes and obesity. The main purposes of our molecular modeling study are to explore the most suitable binding poses of stilbene derivatives with analyzing the binding affinity differences and finally to develop a pharmacophore model which would represents critical features responsible for α-glucosidase inhibitory activity. Three-dimensional structure of S. cerevisiae α-glucosidase was built by homology modeling method and the structure was used for the molecular docking study to find out the initial binding mode of compound 12, which is the most highly active one. The initial structure was subjected to molecular dynamics (MD) simulations for protein structure adjustment at compound 12-bound state. Based on the adjusted conformation, the more reasonable binding modes of the stilbene urea derivatives were obtained from molecular docking and MD simulations. The binding mode of the derivatives was validated by correlation analysis between experimental Ki value and interaction energy. Our results revealed that the binding modes of the potent inhibitors were engaged with important hydrogen bond, hydrophobic, and π-interactions. With the validated compound 12-bound structure obtained from combining approach of docking and MD simulation, a proper four featured pharmacophore model was generated. It was also validated by comparison of fit values with the Ki values. Thus, these results will be helpful for understanding the relationship between binding mode and bioactivity and for designing better inhibitors from stilbene derivatives.

  3. Substrate Binding Mode and its Implication on Drug Design for Botulinum Neurotoxin A

    SciTech Connect

    Kumaran, D.; Rawat, R; Ahmed, A; Swaminathan, S

    2008-01-01

    The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins, the causative agents of botulism, block the neurotransmitter release by specifically cleaving one of the three SNARE proteins and induce flaccid paralysis. The Centers for Disease Control and Prevention (CDC) has declared them as Category A biowarfare agents. The most potent among them, botulinum neurotoxin type A (BoNT/A), cleaves its substrate synaptosome-associated protein of 25 kDa (SNAP-25). An efficient drug for botulism can be developed only with the knowledge of interactions between the substrate and enzyme at the active site. Here, we report the crystal structures of the catalytic domain of BoNT/A with its uncleavable SNAP-25 peptide 197QRATKM202 and its variant 197RRATKM202 to 1.5 A and 1.6 A, respectively. This is the first time the structure of an uncleavable substrate bound to an active botulinum neurotoxin is reported and it has helped in unequivocally defining S1 to S5? sites. These substrate peptides make interactions with the enzyme predominantly by the residues from 160, 200, 250 and 370 loops. Most notably, the amino nitrogen and carbonyl oxygen of P1 residue (Gln197) chelate the zinc ion and replace the nucleophilic water. The P1?-Arg198, occupies the S1? site formed by Arg363, Thr220, Asp370, Thr215, Ile161, Phe163 and Phe194. The S2? subsite is formed by Arg363, Asn368 and Asp370, while S3? subsite is formed by Tyr251, Leu256, Val258, Tyr366, Phe369 and Asn388. P4?-Lys201 makes hydrogen bond with Gln162. P5?-Met202 binds in the hydrophobic pocket formed by the residues from the 250 and 200 loop. Knowledge of interactions between the enzyme and substrate peptide from these complex structures should form the basis for design of potent inhibitors for this neurotoxin.

  4. Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate

    SciTech Connect

    Pazy, Y.; Motaleb, M.A.; Guarnieri, M.T.; Charon, N.W.; Zhao, R.; Silversmith, R.E.

    2010-04-05

    Two-component signal transduction systems are widespread in prokaryotes and control numerous cellular processes. Extensive investigation of sensor kinase and response regulator proteins from many two-component systems has established conserved sequence, structural, and mechanistic features within each family. In contrast, the phosphatases which catalyze hydrolysis of the response regulator phosphoryl group to terminate signal transduction are poorly understood. Here we present structural and functional characterization of a representative of the CheC/CheX/FliY phosphatase family. The X-ray crystal structure of Borrelia burgdorferi CheX complexed with its CheY3 substrate and the phosphoryl analogue BeF{sub 3}{sup -} reveals a binding orientation between a response regulator and an auxiliary protein different from that shared by every previously characterized example. The surface of CheY3 containing the phosphoryl group interacts directly with a long helix of CheX which bears the conserved (E - X{sub 2} - N) motif. Conserved CheX residues Glu96 and Asn99, separated by a single helical turn, insert into the CheY3 active site. Structural and functional data indicate that CheX Asn99 and CheY3 Thr81 orient a water molecule for hydrolytic attack. The catalytic residues of the CheX-CheY3 complex are virtually superimposable on those of the Escherichia coli CheZ phosphatase complexed with CheY, even though the active site helices of CheX and CheZ are oriented nearly perpendicular to one other. Thus, evolution has found two structural solutions to achieve the same catalytic mechanism through different helical spacing and side chain lengths of the conserved acid/amide residues in CheX and CheZ.

  5. Influence of driving frequency on discharge modes in a dielectric-barrier discharge with multiple current pulses

    SciTech Connect

    Jiang, Weiman; Tang, Jie; Wang, Yishan; Zhao, Wei; Duan, Yixiang

    2013-07-15

    A one-dimensional self-consistent fluid model was employed to investigate the effect of the driving frequency on the discharge modes in atmospheric-pressure argon discharge with multiple current pulses. The discharge mode was discussed in detail not only at current peaks but also between two adjacent peaks. The simulation results show that different transitions between the Townsend and glow modes during the discharge take place with the driving frequency increased. A complicated transition from the Townsend mode, through glow, Townsend, and glow, and finally back to the Townsend one is found in the discharge with the driving frequency of 8 kHz. There is a tendency of transition from the Townsend to glow mode for the discharge both at the current peaks and troughs with the increasing frequency. The discharge in the half period can all along operate in the glow mode with the driving frequency high enough. This is resulted from the preservation of more electrons in the gas gap and acquisition of more electron energy from the swiftly varying electric field with the increase in driving frequency. Comparison of the spatial and temporal evolutions of the electron density at different driving frequencies indicates that the increment of the driving frequency allows the plasma chemistry to be enhanced. This electrical characteristic is important for the applications, such as surface treatment and biomedical sterilization.

  6. Multiple binding sites involved in the effect of choline esters on decarbamoylation of monomethylcarbamoyl- or dimethylcarbamoly-acetylcholinesterase.

    PubMed Central

    Sok, D E; Kim, Y B; Choi, S J; Jung, C H; Cha, S H

    1994-01-01

    Multiple binding sites for inhibitory choline esters in spontaneous decarbamoylation of dimethylcarbamoyl-acetylcholinesterase (AChE) were suggested from a wide range of IC50 values, in contrast with a limited range of AC50 values (concentration giving 50% of maximal activation) at a peripheral activatory site. Association of choline esters containing a long acyl chain (C7-C12) with the hydrophobic zone in the active site could be deduced from a linear relationship between the size of the acyl group and the inhibitory potency in either spontaneous decarbamoylation or acetylthiocholine hydrolysis. Direct support for laurylcholine binding to the active site might come from the competitive inhibition (Ki 33 microM) of choline-catalysed decarbamoylation by laurylcholine. Moreover, its inhibitory action was greater for monomethylcarbamoyl-AChE than for dimethylcarbamoyl-AChE, where there is a greater steric hindrance at the active centre. In further support, the inhibition of pentanoylthiocholine-induced decarbamoylation by laurylcholine was suggested to be due to laurylcholine binding to a central site rather than a peripheral site, similar to the inhibition of spontaneous decarbamoylation by laurylcholine. Supportive data for acetylcholine binding to the active site are provided by the results that acetylcholine is a competitive inhibitor (Ki 7.6 mM) of choline-catalysed decarbamoylation, and its inhibitory action was greater for monomethylcarbamoyl-AChE than for dimethylcarbamoyl-AChE. Meanwhile, choline esters with an acyl group of an intermediate size (C4-C6), more subject to steric exclusion at the active centre, and less associable with the hydrophobic zone, appear to bind preferentially to a peripheral activity site. Thus the multiple effects of choline esters may be governed by hydrophobicity and/or a steric effect exerted by the acyl moiety at the binding sites. PMID:8053896

  7. The versatile binding mode of transition-state analogue inhibitors of tyrosinase towards dicopper(II) model complexes: experimental and theoretical investigations.

    PubMed

    Orio, Maylis; Bochot, Constance; Dubois, Carole; Gellon, Gisèle; Hardré, Renaud; Jamet, Hélène; Luneau, Dominique; Philouze, Christian; Réglier, Marius; Serratrice, Guy; Belle, Catherine

    2011-11-25

    We describe 2-mercaptopyridine-N-oxide (HSPNO) as a new and efficient competitive inhibitor of mushroom tyrosinase (K(IC) =3.7 μM). Binding studies of HSPNO and 2-hydroxypyridine-N-oxide (HOPNO) on dinuclear copper(II) complexes [Cu(2)(BPMP)(μ-OH)](ClO(4))(2) (1; HBPMP=2,6-bis[bis(2-pyridylmethyl)aminomethyl]-4-methylphenol) and [Cu(2)(BPEP)(μ-OH)](ClO(4))(2)) (2; HBPEP=2,6-bis{bis[2-(2-pyridyl)ethyl]aminomethyl}-4-methylphenol), known to be functional models for the tyrosinase diphenolase activity, have been performed. A combination of structural data, spectroscopic studies, and DFT calculations evidenced the adaptable binding mode (bridging versus chelating) of HOPNO in relation to the geometry and chelate size of the dicopper center. For comparison, binding studies of HSPNO and kojic acid (5-hydroxy-2-(hydroxymethyl)-4-pyrone) on dinuclear complexes were performed. A theoretical approach has been developed and validated on HOPNO adducts to compare the binding mode on the model complexes. It has been applied for HSPNO and kojic acid. Although results for HSPNO were in line with those obtained with HOPNO, thus reflecting their chemical similarity, we showed that the bridging mode was the most preferential binding mode for kojic acid on both complexes.

  8. Molecular modeling and docking of novel laccase from multiple serotype of Yersinia enterocolitica suggests differential and multiple substrate binding.

    PubMed

    Singh, Deepti; Sharma, Krishna Kant; Dhar, Mahesh Shanker; Virdi, Jugsharan Singh

    2014-06-20

    Multi-copper oxidases (MCOs) are widely distributed in bacteria, where they are responsible for metal homeostasis, acquisition and oxidation. Using specific primers, yacK coding for MCO was amplified from different serotypes of Yersinia enterocolitica biovar 1A. Homology modeling of the protein followed by docking with five well-known substrates for different MCO's (viz., 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid [ABTS], syringaldazine, L-tyrosine, ammonium ferrous sulfate and guaiacol), lignin monomers (Coniferyl alcohol, p-coumaryl alcohol and sinapyl alcohol) and two inhibitors i.e., kojic acid and N-hydroxyglycine was done. The docking gave maximum GoldScore i.e., 91.93 and 72.64 with ammonium ferrous sulfate and ABTS, respectively. Similarly, docking with ICM gave -82.10 and -83.61 docking score, confirming the protein to be true laccase with ferroxidase activity. Further, validation with ammonium ferrous sulfate as substrate gave laccase activity of 0.36Units/L/min. Guaiacol, L-tyrosine, and lignin monomers showed good binding affinity with protein models with GoldScores of 35.89, 41.82, 40.41, 41.12 and 43.10, respectively. The sequence study of all the cloned Yack genes showed serotype specific clade in dendrogram. There was distinct discrimination in the ligand binding affinity of Y. enterocolitica laccase, among strains of same clonal groups, suggesting it as a tool for phylogenetic studies.

  9. Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors

    PubMed Central

    Fang, Bin; Mane-Padros, Daniel; Bolotin, Eugene; Jiang, Tao; Sladek, Frances M.

    2012-01-01

    Nuclear receptors (NRs) regulate gene expression by binding specific DNA sequences consisting of AG[G/T]TCA or AGAACA half site motifs in a variety of configurations. However, those motifs/configurations alone do not adequately explain the diversity of NR function in vivo. Here, a systematic examination of DNA binding specificity by protein-binding microarrays (PBMs) of three closely related human NRs—HNF4α, retinoid X receptor alpha (RXRα) and COUPTF2—reveals an HNF4-specific binding motif (H4-SBM), xxxxCAAAGTCCA, as well as a previously unrecognized polarity in the classical DR1 motif (AGGTCAxAGGTCA) for HNF4α, RXRα and COUPTF2 homodimers. ChIP-seq data indicate that the H4-SBM is uniquely bound by HNF4α but not 10 other NRs in vivo, while NRs PXR, FXRα, Rev-Erbα appear to bind adjacent to H4-SBMs. HNF4-specific DNA recognition and transactivation are mediated by residues Asp69 and Arg76 in the DNA-binding domain; this combination of amino acids is unique to HNF4 among all human NRs. Expression profiling and ChIP data predict ∼100 new human HNF4α target genes with an H4-SBM site, including several Co-enzyme A-related genes and genes with links to disease. These results provide important new insights into NR DNA binding. PMID:22383578

  10. The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-Binding Modes to Diversify Target Recognition.

    PubMed

    Tamayo, Joel V; Teramoto, Takamasa; Chatterjee, Seema; Hall, Traci M Tanaka; Gavis, Elizabeth R

    2017-04-04

    The Drosophila hnRNP F/H homolog, Glorund (Glo), regulates nanos mRNA translation by interacting with a structured UA-rich motif in the nanos 3' untranslated region. Glo regulates additional RNAs, however, and mammalian homologs bind G-tract sequences to regulate alternative splicing, suggesting that Glo also recognizes G-tract RNA. To gain insight into how Glo recognizes both structured UA-rich and G-tract RNAs, we used mutational analysis guided by crystal structures of Glo's RNA-binding domains and identified two discrete RNA-binding surfaces that allow Glo to recognize both RNA motifs. By engineering Glo variants that favor a single RNA-binding mode, we show that a subset of Glo's functions in vivo is mediated solely by the G-tract binding mode, whereas regulation of nanos requires both recognition modes. Our findings suggest a molecular mechanism for the evolution of dual RNA motif recognition in Glo that may be applied to understanding the functional diversity of other RNA-binding proteins.

  11. Screening Mixtures of Small Molecules for Binding to Multiple Sites on the Surface Tetanus Toxin C Fragment by Bioaffinity NMR

    SciTech Connect

    Cosman, M; Zeller, L; Lightstone, F C; Krishnan, V V; Balhorn, R

    2002-01-01

    also contains 3-sialyllactose (another predicted site 1 binder) and bisbenzimide 33342 (non-binder). A series of five predicted Site-2 binders were then screened sequentially in the presence of the Site-1 binder doxorubicin. These experiments showed that the compounds lavendustin A and naphthofluorescein-di-({beta}-D-galactopyranoside) binds along with doxorubicin to TetC. Further experiments indicate that doxorubicin and lavendustin are potential candidates to use in preparing a bidendate inhibitor specific for TetC. The simultaneous binding of two different predicted Site-2 ligands to TetC suggests that they may bind multiple sites. Another possibility is that the conformations of the binding sites are dynamic and can bind multiple diverse ligands at a single site depending on the pre-existing conformation of the protein, especially when doxorubicin is already bound.

  12. A dual-mode bandpass filter with multiple controllable transmission-zeros using T-shaped stub-loaded resonators.

    PubMed

    Yao, Zh; Wang, C; Kim, N Y

    2014-01-01

    A dual-mode broadband bandpass filter (BPF) with multiple controllable transmission-zeros using T-shaped stub-loaded resonators (TSSLRs) is presented. Due to the symmetrical plane, the odd-even-mode theory can be adopted to characterize the BPF. The proposed filter consists of a dual-mode TSSLR and two modified feed-lines, which introduce two capacitive and inductive source-load (S-L) couplings. Five controllable transmission zeros (TZs) can be achieved for the high selectivity and the wide stopband because of the tunable amount of coupling capacitance and inductance. The center frequency of the proposed BPF is 5.8 GHz, with a 3 dB fraction bandwidth of 8.9%. The measured insertion and return losses are 1.75 and 28.18 dB, respectively. A compact size and second harmonic frequency suppression can be obtained by the proposed BPF with S-L couplings.

  13. Sliding mode control for a class of nonlinear discrete-time networked systems with multiple stochastic communication delays

    NASA Astrophysics Data System (ADS)

    Ma, Lifeng; Wang, Zidong; Niu, Yugang; Bo, Yumimg; Guo, Zhi

    2011-04-01

    In this article, a sliding mode control problem is studied for a class of uncertain nonlinear networked systems with multiple communication delays. A sequence of stochastic variables obeying Bernoulli distribution is applied in the system model to describe the randomly occurring communication delays. The discrete-time system considered is also subject to parameter uncertainties and state-dependent stochastic disturbances. A novel discrete switching function is proposed to facilitate the sliding mode controller design. The sufficient conditions are derived by means of the linear matrix inequality (LMI) approach. It is shown that the system dynamics in the specified sliding surface is robustly exponentially stable in the mean square if two LMIs with an equality constraint are feasible. A discrete-time SMC controller is designed that is capable of guaranteeing the discrete-time sliding-mode reaching condition of the specified sliding surface. Finally, a simulation example is given to show the effectiveness of the proposed method.

  14. Characterization of a protein that binds multiple sequences in mammalian type C retrovirus enhancers.

    PubMed Central

    Sun, W; O'Connell, M; Speck, N A

    1993-01-01

    Mammalian type C retrovirus enhancer factor 1 (MCREF-1) is a nuclear protein that binds several directly repeated sequences (CNGGN6CNGG) in the Moloney and Friend murine leukemia virus (MLV) enhancers (N. R. Manley, M. O'Connell, W. Sun, N. A. Speck, and N. Hopkins, J. Virol. 67:1967-1975, 1993). In this paper, we describe the partial purification of MCREF-1 from calf thymus nuclei and further characterize the binding properties of MCREF-1. MCREF-1 binds four sites in the Moloney MLV enhancer and three sites in the Friend MLV enhancer. Ethylation interference analysis suggests that the MCREF-1 binding site spans two adjacent minor grooves of DNA. Images PMID:8445719

  15. Site-directed alkylation of multiple opioid receptors. I. Binding selectivity

    SciTech Connect

    James, I.F.; Goldstein, A.

    1984-05-01

    A method for measuring and expressing the binding selectivity of ligands for mu, delta, and kappa opioid binding sites is reported. Radioligands are used that are partially selective for these sites in combination with membrane preparations enriched in each site. Enrichment was obtained by treatment of membranes with the alkylating agent beta-chlornaltrexamine in the presence of appropriate protecting ligands. After enrichment for mu receptors, (/sup 3/H) dihydromorphine bound to a single type of site as judged by the slope of competition binding curves. After enrichment for delta or kappa receptors, binding sites for (/sup 3/H) (D-Ala2, D-Leu5)enkephalin and (3H)ethylketocyclazocine, respectively, were still not homogeneous. There were residual mu sites in delta-enriched membranes but no evidence for residual mu or delta sites in kappa-enriched membranes were found. This method was used to identify ligands that are highly selective for each of the three types of sites.

  16. Identification of cereblon-binding proteins and relationship with response and survival after IMiDs in multiple myeloma.

    PubMed

    Zhu, Yuan Xiao; Braggio, Esteban; Shi, Chang-Xin; Kortuem, K Martin; Bruins, Laura A; Schmidt, Jessica E; Chang, Xiu-Bao; Langlais, Paul; Luo, Moulun; Jedlowski, Patrick; LaPlant, Betsy; Laumann, Kristina; Fonseca, Rafael; Bergsagel, P Leif; Mikhael, Joseph; Lacy, Martha; Champion, Mia D; Stewart, A Keith

    2014-07-24

    Cereblon (CRBN) mediates immunomodulatory drug (IMiD) action in multiple myeloma (MM). Using 2 different methodologies, we identified 244 CRBN binding proteins and established relevance to MM biology by changes in their abundance after exposure to lenalidomide. Proteins most reproducibly binding CRBN (>fourfold vs controls) included DDB1, CUL4A, IKZF1, KPNA2, LTF, PFKL, PRKAR2A, RANGAP1, and SHMT2. After lenalidomide treatment, the abundance of 46 CRBN binding proteins decreased. We focused attention on 2 of these-IKZF1 and IKZF3. IZKF expression is similar across all MM stages or subtypes; however, IKZF1 is substantially lower in 3 of 5 IMiD-resistant MM cell lines. The cell line (FR4) with the lowest IKZF1 levels also harbors a damaging mutation and a translocation that upregulates IRF4, an IKZF target. Clinical relevance of CRBN-binding proteins was demonstrated in 44 refractory MM patients treated with pomalidomide and dexamethasone therapy in whom low IKZF1 gene expression predicted lack of response (0/11 responses in the lowest expression quartile). CRBN, IKZF1, and KPNA2 levels also correlate with significant differences in overall survival. Our study identifies CRBN-binding proteins and demonstrates that in addition to CRBN, IKZF1, and KPNA2, expression can predict survival outcomes.

  17. Calibration of measurement sensitivities of multiple micro-cantilever dynamic modes in atomic force microscopy using a contact detection method

    SciTech Connect

    Liu Zhen; Jeong, Younkoo; Menq, Chia-Hsiang

    2013-02-15

    An accurate experimental method is proposed for on-spot calibration of the measurement sensitivities of multiple micro-cantilever dynamic modes in atomic force microscopy. One of the key techniques devised for this method is a reliable contact detection mechanism that detects the tip-surface contact instantly. At the contact instant, the oscillation amplitude of the tip deflection, converted to that of the deflection signal in laser reading through the measurement sensitivity, exactly equals to the distance between the sample surface and the cantilever base position. Therefore, the proposed method utilizes the recorded oscillation amplitude of the deflection signal and the base position of the cantilever at the contact instant for the measurement sensitivity calibration. Experimental apparatus along with various signal processing and control modules was realized to enable automatic and rapid acquisition of multiple sets of data, with which the calibration of a single dynamic mode could be completed in less than 1 s to suppress the effect of thermal drift and measurement noise. Calibration of the measurement sensitivities of the first and second dynamic modes of three micro-cantilevers having distinct geometries was successfully demonstrated. The dependence of the measurement sensitivity on laser spot location was also experimentally investigated. Finally, an experiment was performed to validate the calibrated measurement sensitivity of the second dynamic mode of a micro-cantilever.

  18. Calibration of measurement sensitivities of multiple micro-cantilever dynamic modes in atomic force microscopy using a contact detection method.

    PubMed

    Liu, Zhen; Jeong, Younkoo; Menq, Chia-Hsiang

    2013-02-01

    An accurate experimental method is proposed for on-spot calibration of the measurement sensitivities of multiple micro-cantilever dynamic modes in atomic force microscopy. One of the key techniques devised for this method is a reliable contact detection mechanism that detects the tip-surface contact instantly. At the contact instant, the oscillation amplitude of the tip deflection, converted to that of the deflection signal in laser reading through the measurement sensitivity, exactly equals to the distance between the sample surface and the cantilever base position. Therefore, the proposed method utilizes the recorded oscillation amplitude of the deflection signal and the base position of the cantilever at the contact instant for the measurement sensitivity calibration. Experimental apparatus along with various signal processing and control modules was realized to enable automatic and rapid acquisition of multiple sets of data, with which the calibration of a single dynamic mode could be completed in less than 1 s to suppress the effect of thermal drift and measurement noise. Calibration of the measurement sensitivities of the first and second dynamic modes of three micro-cantilevers having distinct geometries was successfully demonstrated. The dependence of the measurement sensitivity on laser spot location was also experimentally investigated. Finally, an experiment was performed to validate the calibrated measurement sensitivity of the second dynamic mode of a micro-cantilever.

  19. Control of focusing fields for positron acceleration in nonlinear plasma wakes using multiple laser modes

    SciTech Connect

    Yu, L.-L. Li, F.-Y.; Chen, M.; Weng, S.-M.; Schroeder, C. B.; Benedetti, C.; Esarey, E.; Sheng, Z.-M.

    2014-12-15

    Control of transverse wakefields in the nonlinear laser-driven bubble regime using a combination of Hermite-Gaussian laser modes is proposed. By controlling the relative intensity ratio of the two laser modes, the focusing force can be controlled, enabling matched beam propagation for emittance preservation. A ring bubble can be generated with a large longitudinal accelerating field and a transverse focusing field suitable for positron beam focusing and acceleration.

  20. Observation of multiple vibrational modes in ultrahigh vacuum tip-enhanced Raman spectroscopy combined with molecular-resolution scanning tunneling microscopy.

    PubMed

    Jiang, N; Foley, E T; Klingsporn, J M; Sonntag, M D; Valley, N A; Dieringer, J A; Seideman, T; Schatz, G C; Hersam, M C; Van Duyne, R P

    2012-10-10

    Multiple vibrational modes have been observed for copper phthalocyanine (CuPc) adlayers on Ag(111) using ultrahigh vacuum (UHV) tip-enhanced Raman spectroscopy (TERS). Several important new experimental features are introduced in this work that significantly advance the state-of-the-art in UHV-TERS. These include (1) concurrent sub-nm molecular resolution STM imaging using Ag tips with laser illumination of the tip-sample junction, (2) laser focusing and Raman collection optics that are external to the UHV-STM that has two cryoshrouds for future low temperature experiments, and (3) all sample preparation steps are carried out in UHV to minimize contamination and maximize spatial resolution. Using this apparatus we have been able to demonstrate a TERS enhancement factor of 7.1 × 10(5). Further, density-functional theory calculations have been carried out that allow quantitative identification of eight different vibrational modes in the TER spectra. The combination of molecular-resolution UHV-STM imaging with the detailed chemical information content of UHV-TERS allows the interactions between large polyatomic molecular adsorbates and specific binding sites on solid surfaces to be probed with unprecedented spatial and spectroscopic resolution.

  1. Dispersion-Tolerant Multiple WDM Channel Millimeter-Wave Signal Generation Using a Single Monolithic Mode-Locked Semiconductor Laser

    NASA Astrophysics Data System (ADS)

    Attygalle, M.; Lim, C.; Nirmalathas, A.

    2005-01-01

    This paper presents a scheme by which multiple wavelength-division-multiplexed millimeter-wave (mm-wave) signals in the range of 30 GHz can be generated from a single monolithic semiconductor laser for applications in optically fed mm-wave networks or fiber radio networks. The mm-wave signals are generated using dual optical modes separated by a mm-wave frequency, obtained from spectrum slicing the output from a stable multimode hybrid mode-locked semiconductor laser. In this scheme, self-heterodyne detection at a high-speed photodetector achieves the photonic upconversion of low-data-rate signals to mm-wave frequencies without the need for electronic mixing. Experimental results show the generation of up to 14 WDM channels using a single laser. The phase noise of electrical signals generated by photonic upconversion of these signals is less than -94 dBc/Hz at 100-kHz offset frequency across the wavelengths. Also presented is the transmission of 155-Mb/s binary-phase-shift-keyed data signals at 30-GHz frequency over 10 km of single-mode fiber at different wavelengths using dual-mode signals. The results confirm that a bit-error rate of 10-^9 can be easily achieved. The dispersion tolerance of the dual-mode signals is evaluated using simulation and an analytical model and compared with other mm-wave signal generation techniques.

  2. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma.

    PubMed

    Gebhard, Anthony W; Jain, Priyesh; Nair, Rajesh R; Emmons, Michael F; Argilagos, Raul F; Koomen, John M; McLaughlin, Mark L; Hazlehurst, Lori A

    2013-11-01

    Our laboratory recently reported that treatment with the d-amino acid containing peptide HYD1 induces necrotic cell death in multiple myeloma cell lines. Because of the intriguing biological activity and promising in vivo activity of HYD1, we pursued strategies for increasing the therapeutic efficacy of the linear peptide. These efforts led to a cyclized peptidomimetic, MTI-101, with increased in vitro activity and robust in vivo activity as a single agent using two myeloma models that consider the bone marrow microenvironment. MTI-101 treatment similar to HYD1 induced reactive oxygen species, depleted ATP levels, and failed to activate caspase-3. Moreover, MTI-101 is cross-resistant in H929 cells selected for acquired resistance to HYD1. Here, we pursued an unbiased chemical biology approach using biotinylated peptide affinity purification and liquid chromatography/tandem mass spectrometry analysis to identify binding partners of MTI-101. Using this approach, CD44 was identified as a predominant binding partner. Reducing the expression of CD44 was sufficient to induce cell death in multiple myeloma cell lines, indicating that multiple myeloma cells require CD44 expression for survival. Ectopic expression of CD44s correlated with increased binding of the FAM-conjugated peptide. However, ectopic expression of CD44s was not sufficient to increase the sensitivity to MTI-101-induced cell death. Mechanistically, we show that MTI-101-induced cell death occurs via a Rip1-, Rip3-, or Drp1-dependent and -independent pathway. Finally, we show that MTI-101 has robust activity as a single agent in the SCID-Hu bone implant and 5TGM1 in vivo model of multiple myeloma.

  3. HPLC-purified 2-(/sup 125/I)iodomelatonin labels multiple binding sites in hamster brain

    SciTech Connect

    Niles, L.P.; Pickering, D.S.; Sayer, B.G.

    1987-09-30

    Binding of 2-(/sup 125/I)iodomelatonin in hamster brain synaptosomal membranes at 0 degrees C is rapid, saturable, reversible and sensitive to heat and trypsin treatment. Computer resolution of curvilinear Scatchard plots yielded high- and low-affinity components as follows: Kd1 = 0.32 +/- 0.14 nM, Bmax1 = 5.6 +/- 1.7 fmol/mg protein and Kd2 = 10.5 +/- 3.2 nM, Bmax2 = 123 +/- 33 fmol/mg protein (n = 3). Competition experiments indicated that 2-iodomelatonin and prazosin are the most potent inhibitors of high-affinity binding. Unlike prazosin, several alpha-adrenergic agents and various neurotransmitters were ineffective. These findings suggest that prazosin may be a potent antagonist at a unique, non-alpha-adrenergic, high-affinity binding site for melatonin.

  4. Neural networks for determining protein specificity and multiple alignment of binding sites

    SciTech Connect

    Heumann, J.M.; Lapedes, A.S.; Stormo, G.D.

    1994-12-31

    We use a quantitative definition of specificity to develop a neural network for the identification of common protein binding sites in a collection of unaligned DNA fragments. We demonstrate the equivalence of the method to maximizing Information Content of the aligned sites when simple models of the binding energy and the genome are employed. The network method subsumes those simple models and is capable of working with more complicated ones. This is demonstrated using a Markov model of the E. coli genome and a sampling method to approximate the partition function. A variation of Gibbs sampling aids in avoiding local minima.

  5. Energy In Action: The Construction Of Physics Ideas In Multiple Modes

    NASA Astrophysics Data System (ADS)

    Close, Eleanor W.; Close, Hunter G.; McKagan, Sarah B.; Scherr, Rachel E.

    2010-10-01

    In a course organized around the development of diverse representations, no single mode of expression offers a complete picture of participants' understanding of the nature of energy. Instead, we argue, their understanding is actively constructed through the simultaneous use of a range of quite different kinds of representational resources (Goodwin, 2000; Hutchins, 1995; Ochs, Gonzales, & Jacoby, 1996), including not only words and prosody but also gestures, symbolic objects, participants moving their bodies in concert, and whatever other communicative modes the course invites them to use. Examples are provided from a teacher professional development course on energy.

  6. Multiple-mode excitation in spin-transfer nanocontacts with dynamic polarizer

    NASA Astrophysics Data System (ADS)

    Wang, N.; Wang, X. L.; Qin, W.; Yeung, S. H.; Kwok, D. T. K.; Wong, H. F.; Xue, Q.; Chu, P. K.; Leung, C. W.; Ruotolo, A.

    2011-06-01

    We report our study on the emission response of a magnetic nanocontact with dynamic polarizer in perpendicular magnetic field. In this configuration three modes are accessible, two of which correspond to the precessional motion of a vortex in one of the two ferromagnetic layers with the other working as a static polarizer. At high currents a third mode can be observed that is ascribed to the simultaneous precession of two vortices, one in each layer, with the other layer working as a dynamic polarizer.

  7. Multiple binding of repressed mRNAs by the P-body protein Rck/p54

    PubMed Central

    Ernoult-Lange, Michèle; Baconnais, Sonia; Harper, Maryannick; Minshall, Nicola; Souquere, Sylvie; Boudier, Thomas; Bénard, Marianne; Andrey, Philippe; Pierron, Gérard; Kress, Michel; Standart, Nancy; le Cam, Eric; Weil, Dominique

    2012-01-01

    Translational repression is achieved by protein complexes that typically bind 3′ UTR mRNA motifs and interfere with the formation of the cap-dependent initiation complex, resulting in mRNPs with a closed-loop conformation. We demonstrate here that the human DEAD-box protein Rck/p54, which is a component of such complexes and central to P-body assembly, is in considerable molecular excess with respect to cellular mRNAs and enriched to a concentration of 0.5 mM in P-bodies, where it is organized in clusters. Accordingly, multiple binding of p54 proteins along mRNA molecules was detected in vivo. Consistently, the purified protein bound RNA with no sequence specificity and high nanomolar affinity. Moreover, bound RNA molecules had a relaxed conformation. While RNA binding was ATP independent, relaxing of bound RNA was dependent on ATP, though not on its hydrolysis. We propose that Rck/p54 recruitment by sequence-specific translational repressors leads to further binding of Rck/p54 along mRNA molecules, resulting in their masking, unwinding, and ultimately recruitment to P-bodies. Rck/p54 proteins located at the 5′ extremity of mRNA can then recruit the decapping complex, thus coupling translational repression and mRNA degradation. PMID:22836354

  8. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes.

    PubMed

    Nandy, Suman Kumar; Seal, Alpana

    2016-01-01

    Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases.

  9. Structural Dynamics Investigation of Human Family 1 & 2 Cystatin-Cathepsin L1 Interaction: A Comparison of Binding Modes

    PubMed Central

    Nandy, Suman Kumar; Seal, Alpana

    2016-01-01

    Cystatin superfamily is a large group of evolutionarily related proteins involved in numerous physiological activities through their inhibitory activity towards cysteine proteases. Despite sharing the same cystatin fold, and inhibiting cysteine proteases through the same tripartite edge involving highly conserved N-terminal region, L1 and L2 loop; cystatins differ widely in their inhibitory affinity towards C1 family of cysteine proteases and molecular details of these interactions are still elusive. In this study, inhibitory interactions of human family 1 & 2 cystatins with cathepsin L1 are predicted and their stability and viability are verified through protein docking & comparative molecular dynamics. An overall stabilization effect is observed in all cystatins on complex formation. Complexes are mostly dominated by van der Waals interaction but the relative participation of the conserved regions varied extensively. While van der Waals contacts prevail in L1 and L2 loop, N-terminal segment chiefly acts as electrostatic interaction site. In fact the comparative dynamics study points towards the instrumental role of L1 loop in directing the total interaction profile of the complex either towards electrostatic or van der Waals contacts. The key amino acid residues surfaced via interaction energy, hydrogen bonding and solvent accessible surface area analysis for each cystatin-cathepsin L1 complex influence the mode of binding and thus control the diverse inhibitory affinity of cystatins towards cysteine proteases. PMID:27764212

  10. Development of a Competitive Binding Assay System with Recombinant Estrogen Receptors from Multiple Species

    EPA Science Inventory

    ABSTRACT In the current study, we developed a new system using full-length recombinant baculovirus-expressed estrogen receptors which allows for direct comparison of binding across species. Estrogen receptors representing five vertebrate classes were compared: human (hERα), quai...

  11. Binding of Multiple Features in Memory by High-Functioning Adults with Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Bowler, Dermot M.; Gaigg, Sebastian B.; Gardiner, John M.

    2014-01-01

    Diminished episodic memory and diminished use of semantic information to aid recall by individuals with autism spectrum disorder (ASD) are both thought to result from diminished relational binding of elements of complex stimuli. To test this hypothesis, we asked high-functioning adults with ASD and typical comparison participants to study grids in…

  12. Multiple roles for polypyrimidine tract binding (PTB) proteins in trypanosome RNA metabolism

    PubMed Central

    Stern, Michael Zeev; Gupta, Sachin Kumar; Salmon-Divon, Mali; Haham, Tomer; Barda, Omer; Levi, Sarit; Wachtel, Chaim; Nilsen, Timothy W.; Michaeli, Shulamit

    2009-01-01

    Trypanosomatid genomes encode for numerous proteins containing an RNA recognition motif (RRM), but the function of most of these proteins in mRNA metabolism is currently unknown. Here, we report the function of two such proteins that we have named PTB1 and PTB2, which resemble the mammalian polypyrimidine tract binding proteins (PTB). RNAi silencing of these factors indicates that both are essential for life. PTB1 and PTB2 reside mostly in the nucleus, but are found in the cytoplasm, as well. Microarray analysis performed on PTB1 and PTB2 RNAi silenced cells indicates that each of these factors differentially affects the transcriptome, thus regulating a different subset of mRNAs. PTB1 and PTB2 substrates were categorized bioinformatically, based on the presence of PTB binding sites in their 5′ and 3′ flanking sequences. Both proteins were shown to regulate mRNA stability. Interestingly, PTB proteins are essential for trans-splicing of genes containing C-rich polypyrimidine tracts. PTB1, but not PTB2, also affects cis-splicing. The specificity of binding of PTB1 was established in vivo and in vitro using a model substrate. This study demonstrates for the first time that trans-splicing of only certain substrates requires specific factors such as PTB proteins for their splicing. The trypanosome PTB proteins, like their mammalian homologs, represent multivalent RNA binding proteins that regulate mRNAs from their synthesis to degradation. PMID:19218552

  13. Structure of Bacillus subtilis γ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

    SciTech Connect

    Ida, Tomoyo; Suzuki, Hideyuki; Fukuyama, Keiichi; Hiratake, Jun; Wada, Kei

    2014-02-01

    The binding modes of acivicin, a classical and an electrophilic active-site-directed glutamate analogue, to bacterial γ-glutamyltranspeptidases were found to be diverse. γ-Glutamyltranspeptidase (GGT) is an enzyme that plays a central role in glutathione metabolism, and acivicin is a classical inhibitor of GGT. Here, the structure of acivicin bound to Bacillus subtilis GGT determined by X-ray crystallography to 1.8 Å resolution is presented, in which it binds to the active site in a similar manner to that in Helicobacter pylori GGT, but in a different binding mode to that in Escherichia coli GGT. In B. subtilis GGT, acivicin is bound covalently through its C3 atom with sp{sup 2} hybridization to Thr403 O{sup γ}, the catalytic nucleophile of the enzyme. The results show that acivicin-binding sites are common, but the binding manners and orientations of its five-membered dihydroisoxazole ring are diverse in the binding pockets of GGTs.

  14. Dual-mode on-demand droplet routing in multiple microchannels using a magnetic fluid as carrier phase.

    PubMed

    Kim, Jitae; Won, June; Song, Simon

    2014-09-01

    We present dual-mode, on-demand droplet routing in a multiple-outlet microfluidic device using an oil-based magnetic fluid. Magnetite (Fe3O4) nanoparticle-contained oleic acid (MNOA) was used as a carrier phase for droplet generation and manipulation. The water-in-MNOA droplets were selectively distributed in a curved microchannel with three branches by utilizing both a hydrodynamic laminar flow pattern and an external magnetic field. Without the applied magnetic field, the droplets travelled along a hydrodynamic centerline that was displaced at each bifurcating junction. However, in the presence of a permanent magnet, they were repelled from the centerline and diverted into the desired channel when the repelled distance exceeded the minimum offset allocated to the channel. The repelled distance, which is proportional to the magnetic field gradient, was manipulated by controlling the magnet's distance from the device. To evaluate routing performance, three different sizes of droplets with diameters of 63, 88, and 102 μm were directed into designated outlets with the magnet positioned at varying distances. The result demonstrated that the 102-μm droplets were sorted with an accuracy of ∼93%. Our technique enables on-demand droplet routing in multiple outlet channels by simply manipulating magnet positions (active mode) as well as size-based droplet separation with a fixed magnet position (passive mode).

  15. Mode structure in the far field radiation of a leaky-wave multiple quantum well laser

    SciTech Connect

    Nekorkin, S M; Zvonkov, B N; Karzanova, Maria V; Dikareva, Natalia V; Aleshkin, V Ya; Dubinov, A A

    2012-10-31

    The radiation patterns of a leaky-wave InGaAs/GaAs/InGaP laser are studied. In the subthreshold regime, several peaks are found, corresponding to the emission of fundamental and excited modes. The dependences of the amplitude, position and width of the peaks on the pump current are investigated and explained. (measurement of laser radiation parameters)

  16. Acoustic fatigue life prediction for nonlinear structures with multiple resonant modes

    NASA Astrophysics Data System (ADS)

    Miles, R. N.

    1992-03-01

    This report documents an effort to develop practical and accurate methods for estimating the fatigue lives of complex aerospace structures subjected to intense random excitations. The emphasis of the current program is to construct analytical schemes for performing fatigue life estimates for structures that exhibit nonlinear vibration behavior and that have numerous resonant modes contributing to the response.

  17. Acoustic fatigue life prediction for nonlinear structures with multiple resonant modes

    NASA Technical Reports Server (NTRS)

    Miles, R. N.

    1992-01-01

    This report documents an effort to develop practical and accurate methods for estimating the fatigue lives of complex aerospace structures subjected to intense random excitations. The emphasis of the current program is to construct analytical schemes for performing fatigue life estimates for structures that exhibit nonlinear vibration behavior and that have numerous resonant modes contributing to the response.

  18. Pro-oxidant copper-binding mode of the Apo form of ALS-linked SOD1 mutant H43R denatured at physiological temperature.

    PubMed

    Fujimaki, Nobuhiro; Kitamura, Furi; Takeuchi, Hideo

    2013-08-06

    The mutation of Cu,Zn-superoxide dismutase (SOD1), a major antioxidant enzyme, is associated with amyotrophic lateral sclerosis (ALS). In a previous study, we showed that the metal-depleted apo form of an ALS-linked mutant, H43R, undergoes denaturation at physiological temperature (37 °C) in 90 min and acquires pro-oxidant activity in the presence of Cu(2+) and H2O2. In this study, we have examined the Cu(2+)-binding mode of denatured apo-H43R by circular dichroism (CD), fluorescent oxidation, UV Raman spectroscopy, and photooxidation. CD spectroscopy indicates that denatured apo-H43R loses native β-barrel structure and the binding of Cu(2+) to the denatured apo form induces local refolding. Fluorescent-oxidation assays in the absence and presence of Cu(2+) chelators show that denatured apo-H43R contains two Cu(2+)-binding sites with higher and lower Cu(2+) affinities and with pro-oxidant activities in the reverse order. UV Raman spectroscopy gives evidence that His residues are bound to Cu(2+) mainly through the imidazole Nτ atom at the higher-affinity site and through the Nπ atom at the lower-affinity site, sharing one His residue with each other. The Cu(2+)-binding mode of denatured apo-H43R is analogous to but different from the Cu,Zn-binding mode of the native holo form. Photooxidation experiments confirm the involvement of His residues in the pro-oxidant activity. Taken together, it is suggested that the binding of Cu(2+) induces the local refolding of denatured apo-H43R to create toxic catalytic centers that convert the enzyme from antioxidant to pro-oxidant, leading to the pathogenesis of ALS. His residues are essential for both Cu(2+)-binding and pro-oxidant activities.

  19. Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation

    NASA Astrophysics Data System (ADS)

    ter Laak, Anton M.; Timmerman, Hendrik; Leurs, Rob; Nederkoorn, Paul H. J.; Smit, Martine J.; Donné-Op den Kelder, Gabriëlle M.

    1995-08-01

    A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H1-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys200, Thr203 and Asn207, for which a functional role in binding has been proposed. The most favourable results were obtained for the interaction between Hist and the Lys200/Asn207 pair. Therefore, Lys200 was subsequently mutated and converted to an alanine, resulting in a 50-fold decrease of H1-receptor stimulation by histamine. Altogether, the data suggest that the Lys200/Asn207 pair is important for activation of the H1-receptor by histamine. In contrast, analogues of 2-PhHist seem to belong to a distinct subclass of histamine agonists and an alternative mode of binding is proposed in which the 2-phenyl ring binds to the same receptor location as one of the aromatic rings of classical histamine H1-antagonists. Subsequently, the binding modes of the agonists Hist, 2-MeHist and 2-PhHist and the H1-antagonist cyproheptadine were evaluated in three different seven-α-helical models of the H1-receptor built in homology with bacteriorhodopsin, but using three different alignments. Our findings suggest that the position of the carboxylate group of Asp116 (TM3) within the receptor pocket depends on whether an agonist or an antagonist binds to the protein; a conformational change of this aspartate residue upon agonist binding is expected to play an essential role in receptor stimulation.

  20. Multiple changes of penicillin-binding proteins in penicillin-resistant clinical isolates of Streptococcus pneumoniae.

    PubMed Central

    Hakenbeck, R; Tarpay, M; Tomasz, A

    1980-01-01

    Penicillin-binding properties and characteristics of penicillin-binding proteins (PBPs) were investigated in several clinical isolates of Streptococcus pneumoniae differing in their susceptibilities to penicillin (minimal inhibitory concentration [MIC], 0.03 to 0.5 microgram/ml) and compared with the penicillin-susceptible strain R36A (MIC, 0.07 microgram/ml). Several changes accompanied the development of resistance: the relative affinity to penicillin of whole cells, isolated membranes, and two major PBPs after in vivo or in vitro labeling decreased (with increasing resistance). Furthermore, one additional PBP (2') appeared in four of five relatively resistant strains with an MIC of 0.25 microgram/ml and higher. PBP 3 maintained the same high affinity toward penicillin in all strains under all labeling conditions. Images PMID:7425601

  1. Supramolecular Polymers with Multiple Types of Binding Motifs: From Fundamental Studies to Multifunctional Materials

    DTIC Science & Technology

    2015-07-10

    the goal of preparing multi-responsive polymer actuators, we have incorporated liquid crystalline metal-binding Bip monomers into polymeric networks...SECURITY CLASSIFICATION OF: This research project is focused on the development and investigation of a new class of multi-stimuli-responsive polymers ...studies metallo and hydrogen bonded supramolecular polymers that exhibit defect healing characteristics and multi- 1. REPORT DATE (DD-MM-YYYY) 4

  2. Identification of multiple salicylic acid-binding proteins using two high throughput screens

    PubMed Central

    Manohar, Murli; Tian, Miaoying; Moreau, Magali; Park, Sang-Wook; Choi, Hyong Woo; Fei, Zhangjun; Friso, Giulia; Asif, Muhammed; Manosalva, Patricia; von Dahl, Caroline C.; Shi, Kai; Ma, Shisong; Dinesh-Kumar, Savithramma P.; O'Doherty, Inish; Schroeder, Frank C.; van Wijk, Klass J.; Klessig, Daniel F.

    2014-01-01

    Salicylic acid (SA) is an important hormone involved in many diverse plant processes, including floral induction, stomatal closure, seed germination, adventitious root initiation, and thermogenesis. It also plays critical functions during responses to abiotic and biotic stresses. The role(s) of SA in signaling disease resistance is by far the best studied process, although it is still only partially understood. To obtain insights into how SA carries out its varied functions, particularly in activating disease resistance, two new high throughput screens were developed to identify novel SA-binding proteins (SABPs). The first utilized crosslinking of the photo-reactive SA analog 4-AzidoSA (4AzSA) to proteins in an Arabidopsis leaf extract, followed by immuno-selection with anti-SA antibodies and then mass spectroscopy-based identification. The second utilized photo-affinity crosslinking of 4AzSA to proteins on a protein microarray (PMA) followed by detection with anti-SA antibodies. To determine whether the candidate SABPs (cSABPs) obtained from these screens were true SABPs, recombinantly-produced proteins were generated and tested for SA-inhibitable crosslinking to 4AzSA, which was monitored by immuno-blot analysis, SA-inhibitable binding of the SA derivative 3-aminoethylSA (3AESA), which was detected by a surface plasmon resonance (SPR) assay, or SA-inhibitable binding of [3H]SA, which was detected by size exclusion chromatography. Based on our criteria that true SABPs must exhibit SA-binding activity in at least two of these assays, nine new SABPs are identified here; nine others were previously reported. Approximately 80 cSABPs await further assessment. In addition, the conflicting reports on whether NPR1 is an SABP were addressed by showing that it bound SA in all three of the above assays. PMID:25628632

  3. Coupled multiple-mode theory for s± pairing mechanism in iron based superconductors.

    PubMed

    Kiselev, M N; Efremov, D V; Drechsler, S L; van den Brink, Jeroen; Kikoin, K

    2016-11-29

    We investigate the interplay between the magnetic and the superconducting degrees of freedom in unconventional multi-band superconductors such as iron pnictides. For this purpose a dynamical mode-mode coupling theory is developed based on the coupled Bethe-Salpeter equations. In order to investigate the region of the phase diagram not too far from the tetracritical point where the magnetic spin density wave, (SDW) and superconducting (SC) transition temperatures coincide, we also construct a Ginzburg-Landau functional including both SC and SDW fluctuations in a critical region above the transition temperatures. The fluctuation corrections tend to suppress the magnetic transition, but in the superconducting channel the intraband and interband contribution of the fluctuations nearly compensate each other.

  4. Coupled multiple-mode theory for s± pairing mechanism in iron based superconductors

    PubMed Central

    Kiselev, M. N.; Efremov, D. V.; Drechsler, S. L.; van den Brink, Jeroen; Kikoin, K.

    2016-01-01

    We investigate the interplay between the magnetic and the superconducting degrees of freedom in unconventional multi-band superconductors such as iron pnictides. For this purpose a dynamical mode-mode coupling theory is developed based on the coupled Bethe-Salpeter equations. In order to investigate the region of the phase diagram not too far from the tetracritical point where the magnetic spin density wave, (SDW) and superconducting (SC) transition temperatures coincide, we also construct a Ginzburg-Landau functional including both SC and SDW fluctuations in a critical region above the transition temperatures. The fluctuation corrections tend to suppress the magnetic transition, but in the superconducting channel the intraband and interband contribution of the fluctuations nearly compensate each other. PMID:27897177

  5. Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold with an Unusual Mode of Binding

    SciTech Connect

    Sidote,D.; Barbieri, C.; Wu, T.; Stock, A.

    2008-01-01

    The LytTR domain is a DNA-binding motif found within the AlgR/AgrA/LytR family of transcription factors that regulate virulence factor and toxin gene expression in pathogenic bacteria. This previously uncharacterized domain lacks sequence similarity with proteins of known structure. The crystal structure of the DNA-binding domain of Staphylococcus aureus AgrA complexed with a DNA pentadecamer duplex has been determined at 1.6 Angstroms resolution. The structure establishes a 10-stranded {beta} fold for the LytTR domain and reveals its mode of interaction with DNA. Residues within loop regions of AgrA contact two successive major grooves and the intervening minor groove on one face of the oligonucleotide duplex, inducing a substantial bend in the DNA. Loss of DNA binding upon substitution of key interacting residues in AgrA supports the observed binding mode. This mode of protein-DNA interaction provides a potential target for future antimicrobial drug design.

  6. Polymeric ion sensors with multiple detection modes achieved by a new type of click chemistry reaction.

    PubMed

    Michinobu, Tsuyoshi; Li, Yongrong; Hyakutake, Tsuyoshi

    2013-02-28

    The rapid growth of the click chemistry concept enables the production of a wide variety of functional polymers. Among the new generation of click chemistry reactions, the highly efficient addition reactions between electron-rich alkynes and cyano-based acceptors, referred to as alkyne-acceptor click chemistry, have found promising application possibilities as polymeric chemosensors. The donor-acceptor chromophores, formed by this click chemistry reaction, feature intense charge-transfer (CT) bands in the visible region, but they are hardly fluorescent. Importantly, the chromophores possess two different nitrogen atoms, namely the aniline nitrogen and cyano nitrogen. The recognition of some specific metal cations by different nitrogen atoms in the polymers led to different modes of changes in the absorption spectra. For example, the hard acid of Fe(3+) ion was recognized by the aniline nitrogen, resulting in a decrease in the CT bands. On the other hand, the soft acid of the Ag(+) ion was captured by the cyano nitrogen, leading to a bathochromic shift in the CT bands. Some specific anions, such as CN(-), F(-), and I(-) ions, were also recognized by a chemodocimetric detection mode, discoloring the original solutions. When the CT bands decreased upon the addition of analytes, the polymers were found to serve as turn-on fluorescent sensors. In this perspective, the detailed detection modes of the new polymeric chemosensors are fully described.

  7. Quantitative analysis of multiple components based on liquid chromatography with mass spectrometry in full scan mode.

    PubMed

    Xu, Min Li; Li, Bao Qiong; Wang, Xue; Chen, Jing; Zhai, Hong Lin

    2016-08-01

    Although liquid chromatography with mass spectrometry in full scan mode can obtain all the signals simultaneously in a large range and low cost, it is rarely used in quantitative analysis due to several problems such as chromatographic drifts and peak overlap. In this paper, we propose a Tchebichef moment method for the simultaneous quantitative analysis of three active compounds in Qingrejiedu oral liquid based on three-dimensional spectra in full scan mode of liquid chromatography with mass spectrometry. After the Tchebichef moments were calculated directly from the spectra, the quantitative linear models for three active compounds were established by stepwise regression. All the correlation coefficients were more than 0.9978. The limits of detection and limits of quantitation were less than 0.11 and 0.49 μg/mL, respectively. The intra- and interday precisions were less than 6.54 and 9.47%, while the recovery ranged from 102.56 to 112.15%. Owing to the advantages of multi-resolution and inherent invariance properties, Tchebichef moments could provide favorable results even in the situation of peaks shifting and overlapping, unknown interferences and noise signals, so it could be applied to the analysis of three-dimensional spectra in full scan mode of liquid chromatography with mass spectrometry.

  8. System Reliability Assessment for a Rock Tunnel with Multiple Failure Modes

    NASA Astrophysics Data System (ADS)

    Lü, Qing; Chan, Chin Loong; Low, Bak Kong

    2013-07-01

    This paper presents a practical procedure for assessing the system reliability of a rock tunnel. Three failure modes, namely, inadequate support capacity, excessive tunnel convergence, and insufficient rockbolt length, are considered and investigated using a deterministic model of ground-support interaction analysis based on the convergence-confinement method (CCM). The failure probability of each failure mode is evaluated from the first-order reliability method (FORM) and the response surface method (RSM) via an iterative procedure. The system failure probability bounds are estimated using the bimodal bounds approach suggested by Ditlevsen (1979), based on the reliability index and design point inferred from the FORM. The proposed approach is illustrated with an example of a circular rock tunnel. The computed system failure probability bounds compare favorably with those generated from Monte Carlo simulations. The results show that the relative importance of different failure modes to the system reliability of the tunnel mainly depends on the timing of support installation relative to the advancing tunnel face. It is also shown that reliability indices based on the second-order reliability method (SORM) can be used to achieve more accurate bounds on the system failure probability for nonlinear limit state surfaces. The system reliability-based design for shotcrete thickness is also demonstrated.

  9. Feasibility of large volume tumor ablation using multiple-mode strategy with fast scanning method: A numerical study

    NASA Astrophysics Data System (ADS)

    Wu, Hao; Shen, Guofeng; Qiao, Shan; Chen, Yazhu

    2017-03-01

    Sonication with fast scanning method can generate homogeneous lesions without complex planning. But when the target region is large, switching focus too fast will reduce the heat accumulation, the margin of which may not ablated. Furthermore, high blood perfusion rate will reduce this maximum volume that can be ablated. Therefore, fast scanning method may not be applied to large volume tumor. To expand the therapy scope, this study combines the fast scan method with multiple mode strategy. Through simulation and experiment, the feasibility of this new strategy is evaluated and analyzed.

  10. Discovery of multiple, ionization-created CS{sub 2} anions and a new mode of operation for drift chambers

    SciTech Connect

    Snowden-Ifft, Daniel P.

    2014-01-15

    This paper focuses on the surprising discovery of multiple species of ionization-created CS{sub 2} anions in gas mixtures containing electronegative CS{sub 2} and O{sub 2}, identified by their slightly different drift velocities. Data are presented to understand the formation mechanism and identity of these new anions. Regardless of the micro-physics, however, this discovery offers a new, trigger-less mode of operation for the drift chambers. A demonstration of trigger-less operation is presented.

  11. Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: characterization of an active site isoleucine.

    PubMed

    Boulanger, Martin J; Murphy, Michael E P

    2003-02-01

    Unlike the heme cd(1)-based nitrite reductase enzymes, the molecular mechanism of copper-containing nitrite reductases remains controversial. A key source of controversy is the productive binding mode of nitrite in the active site. To identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257 in nitrite reductase from Alcaligenes faecalis S-6. The activities of these six variants span nearly two orders of magnitude with one variant, I257V, the only observed natural substitution for Ile257, showing greater activity than the native enzyme. High-resolution (> 1.8 A) nitrite-soaked crystal structures of these variants display different modes of nitrite binding that correlate well with the altered activities. These studies identify for the first time that the highly conserved Ile257 in the native enzyme is a key molecular determinant in directing a catalytically competent mode of nitrite binding in the active site. The O-coordinate bidentate binding mode of nitrite observed in native and mutant forms with high activity supports a catalytic model distinct from the heme cd(1) NiRs. (The atomic coordinates for I257V[NO(2)(-)], I257L[NO(2)(-)], I257A[NO(2)(-)], I257T[NO(2)(-)], I257M[NO(2)(-)] and I257G[NO(2)(-)] AfNiR have been deposited in the Protein Data Bank [PDB identification codes are listed in Table 2].)

  12. A solution NMR study of the interactions of oligomannosides and the anti-HIV-1 2G12 antibody reveals distinct binding modes for branched ligands.

    PubMed

    Enríquez-Navas, Pedro M; Marradi, Marco; Padro, Daniel; Angulo, Jesús; Penadés, Soledad

    2011-02-01

    The structural and affinity details of the interactions of synthetic oligomannosides, linear (di-, tri-, and tetra-) and branched (penta- and hepta-), with the broadly neutralizing anti-HIV-1 antibody 2G12 (HIV=human immunodeficiency virus) have been investigated in solution by using ligand-based NMR techniques, specifically saturation transfer difference (STD) NMR spectroscopy and transferred NOE experiments. Linear oligomannosides show similar binding modes to the antibody, with the nonreducing terminal disaccharide Manα(1→2)Man (Man=mannose) making the closest protein/ligand contacts in the bound state. In contrast, the branched pentamannoside shows two alternate binding modes, involving both ligand arms (D2- and D3-like), a dual binding description of the molecular recognition of this ligand by 2G12 in solution that differs from the single binding mode deduced from X-ray studies. On the contrary, the antibody shows an unexpected selectivity for one arm (D1-like) of the other branched ligand (heptamannoside). This result explains the previously reported lack of affinity enhancement relative to that of the D1-like tetramannoside. Single-ligand STD NMR titration experiments revealed noticeable differences in binding affinities among the linear and branched ligands in solution, with the latter showing decreased affinity. Among the analyzed series of ligands, the strongest 2G12 binders were the linear tri- and tetramannosides because both show similar affinity for the antibody. These results demonstrate that NMR spectroscopic techniques can deliver abundant structural, dynamics, and affinity information for the characterization of oligomannose-2G12 binding in solution, thus complementing, and, as in the case of the pentamannoside, extending, the structural view from X-ray crystallography. This information is of key importance for the development of multivalent synthetic gp120 high-mannose glycoconjugate mimics in the context of vaccine development.

  13. The Binding Mode of Second-Generation Sulfonamide Inhibitors of MurD: Clues for Rational Design of Potent MurD Inhibitors

    PubMed Central

    Simčič, Mihael; Sosič, Izidor; Hodošček, Milan; Barreteau, Hélène; Blanot, Didier; Gobec, Stanislav; Grdadolnik, Simona Golič

    2012-01-01

    A series of optimized sulfonamide derivatives was recently reported as novel inhibitors of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD). These are based on naphthalene-N-sulfonyl-D-glutamic acid and have the D-glutamic acid replaced with rigidified mimetics. Here we have defined the binding site of these novel ligands to MurD using 1H/13C heteronuclear single quantum correlation. The MurD protein was selectively 13C-labeled on the methyl groups of Ile (δ1 only), Leu and Val, and was isolated and purified. Crucial Ile, Leu and Val methyl groups in the vicinity of the ligand binding site were identified by comparison of chemical shift perturbation patterns among the ligands with various structural elements and known binding modes. The conformational and dynamic properties of the bound ligands and their binding interactions were examined using the transferred nuclear Overhauser effect and saturation transfer difference. In addition, the binding mode of these novel inhibitors was thoroughly examined using unrestrained molecular dynamics simulations. Our results reveal the complex dynamic behavior of ligand–MurD complexes and its influence on ligand–enzyme contacts. We further present important findings for the rational design of potent Mur ligase inhibitors. PMID:23285193

  14. Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-Binding Sites Involved in Nuclear Export.

    PubMed

    Port, Sarah A; Monecke, Thomas; Dickmanns, Achim; Spillner, Christiane; Hofele, Romina; Urlaub, Henning; Ficner, Ralf; Kehlenbach, Ralph H

    2015-10-27

    CRM1 is the major nuclear export receptor. During translocation through the nuclear pore, transport complexes transiently interact with phenylalanine-glycine (FG) repeats of multiple nucleoporins. On the cytoplasmic side of the nuclear pore, CRM1 tightly interacts with the nucleoporin Nup214. Here, we present the crystal structure of a 117-amino-acid FG-repeat-containing fragment of Nup214, in complex with CRM1, Snurportin 1, and RanGTP at 2.85 Å resolution. The structure reveals eight binding sites for Nup214 FG motifs on CRM1, with intervening stretches that are loosely attached to the transport receptor. Nup214 binds to N- and C-terminal regions of CRM1, thereby clamping CRM1 in a closed conformation and stabilizing the export complex. The role of conserved hydrophobic pockets for the recognition of FG motifs was analyzed in biochemical and cell-based assays. Comparative studies with RanBP3 and Nup62 shed light on specificities of CRM1-nucleoporin binding, which serves as a paradigm for transport receptor-nucleoporin interactions.

  15. A DNA-binding Molecule Targeting the Adaptive Hypoxic Response in Multiple Myeloma has Potent Anti-tumor Activity

    PubMed Central

    Mysore, Veena S.; Szablowski, Jerzy; Dervan, Peter B.; Frost, Patrick J.

    2016-01-01

    Multiple myeloma (MM) is incurable and invariably becomes resistant to chemotherapy. Although the mechanisms remain unclear, hypoxic conditions in the bone marrow have been implicated in contributing to MM progression, angiogenesis, and resistance to chemotherapy. These effects occur via adaptive cellular responses mediated by hypoxia-inducible transcription factors (HIFs), and targeting HIFs can have anti-cancer effects in both solid and hematological malignancies. Here, it was found that in most myeloma cell lines tested, HIF1α, but not HIF2α expression was oxygen dependent and this could be explained by the differential expression of the regulatory prolyl-hydroxylase isoforms. The anti-MM effects of a sequence-specific DNA-binding pyrrole-imidazole polyamide (HIF-PA), that disrupts the HIF heterodimer from binding to its cognate DNA sequences, were also investigated. HIF-PA is cell permeable, localizes to the nuclei, and binds specific regions of DNA with an affinity comparable to that of HIF transcription factors. Most of the MM cells were resistant to hypoxia-mediated apoptosis, and HIF-PA treatment could overcome this resistance in vitro. Using xenograft models, it was determined that HIF-PA significantly decreased tumor volume and increased hypoxic and apoptotic regions within solid tumor nodules and the growth of myeloma cells engrafted in the bone marrow. This provides a rationale for targeting the adaptive cellular hypoxic response of the O2-dependent activation of HIFα using polyamides. PMID:26801054

  16. The glutathione conjugate of ethacrynic acid can bind to human pi class glutathione transferase P1-1 in two different modes.

    PubMed

    Oakley, A J; Lo Bello, M; Mazzetti, A P; Federici, G; Parker, M W

    1997-12-08

    The diuretic drug ethacrynic acid, an inhibitor of pi class glutathione S-transferase, has been tested in clinical trials as an adjuvant in chemotherapy. We recently solved the crystal structure of this enzyme in complex with ethacrynic acid and its glutathione conjugate. Here we present a new structure of the ethacrynic-glutathione conjugate complex. In this structure the ethacrynic moiety of the complex is shown to bind in a completely different orientation to that previously observed. Thus there are at least two binding modes possible, an observation of great importance to the design of second generation inhibitors of the enzyme.

  17. Multiple mode x-ray ptychography using a lens and a fixed diffuser optic

    NASA Astrophysics Data System (ADS)

    Li, Peng; Batey, Darren J.; Edo, Tega B.; Parsons, Aaron D.; Rau, Christoph; Rodenburg, John M.

    2016-05-01

    We employ a novel combination of a Fresnel lens and a diffuser for x-ray ptychography. The setup uses increased flux by enlarging the width of the coherence-defining slits upstream of the experimental station. In the reconstruction algorithm, modal decomposition is used to account for the resulting partial coherence in the beam. We show that if the object has sparse feactures and large areas of flat contrast, the diffuser facilitates a better reconstruction and the extra diversity in the data also allows cleaner separation of the constituent modes in the illumination. The setup also allows a quick, real-time measure of the beam coherence.

  18. MTI-101 (cyclized HYD1) binds a CD44 containing complex and induces necrotic cell death in multiple myeloma

    PubMed Central

    Gebhard, Anthony W.; Jain, Priyesh; Nair, Rajesh R.; Emmons, Michael F.; Argilagos, Raul F.; Koomen, John M.; McLaughlin, Mark L.; Hazlehurst, Lori A.

    2013-01-01

    Our laboratory recently reported that treatment with the d-amino acid containing peptide HYD1 induces necrotic cell death in multiple myeloma (MM) cell lines. Due to the intriguing biological activity and promising in vivo activity of HYD1, we pursued strategies for increasing the therapeutic efficacy of the linear peptide. These efforts led to a cyclized peptidomimetic, MTI-101, with increased in vitro activity and robust in vivo activity as single agent using two myeloma models that consider the bone marrow microenvironment. MTI-101 treatment similar to HYD1 induced reactive oxygen species, depleted ATP levels and failed to activate caspase 3. Moreover, MTI-101 is cross-resistant in H929 cells selected for acquired resistance to HYD1. Here, we pursued an unbiased chemical biology approach using biotinylated peptide affinity purification and LC-MS/MS analysis to identify binding partners of MTI-101. Using this approach CD44 was identified as a predominant binding partner. Reducing the expression of CD44 was sufficient to induce cell death in MM cell lines, indicating that MM cells require CD44 expression for survival. Ectopic expression of CD44s correlated with increased binding of the FAM-conjugated peptide. However ectopic expression of CD44s was not sufficient to increase the sensitivity to MTI-101 induced cell death. Mechanistically, we show that MTI-101 induced cell death occurs via a Rip1, Rip3 or Drp1 dependent and independent pathway. Finally, we show that MTI-101 has robust activity as a single agent in the SCID-Hu bone implant and 5TGM1 in vivo model of multiple myeloma. PMID:24048737

  19. Long-term music training tunes how the brain temporally binds signals from multiple senses.

    PubMed

    Lee, Hweeling; Noppeney, Uta

    2011-12-20

    Practicing a musical instrument is a rich multisensory experience involving the integration of visual, auditory, and tactile inputs with motor responses. This combined psychophysics-fMRI study used the musician's brain to investigate how sensory-motor experience molds temporal binding of auditory and visual signals. Behaviorally, musicians exhibited a narrower temporal integration window than nonmusicians for music but not for speech. At the neural level, musicians showed increased audiovisual asynchrony responses and effective connectivity selectively for music in a superior temporal sulcus-premotor-cerebellar circuitry. Critically, the premotor asynchrony effects predicted musicians' perceptual sensitivity to audiovisual asynchrony. Our results suggest that piano practicing fine tunes an internal forward model mapping from action plans of piano playing onto visible finger movements and sounds. This internal forward model furnishes more precise estimates of the relative audiovisual timings and hence, stronger prediction error signals specifically for asynchronous music in a premotor-cerebellar circuitry. Our findings show intimate links between action production and audiovisual temporal binding in perception.

  20. Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes

    SciTech Connect

    Dahms, Sven O.; Mayer, Magnus C.; Roeser, Dirk; Multhaup, Gerd; Than, Manuel E.

    2015-03-01

    Two X-ray structures of APLP1 E2 with and without a heparin dodecasaccharide are presented, revealing two distinct binding modes of the protein to heparan sulfate. The data provide a mechanistic explanation of how APP-like proteins bind to heparan sulfates and how they specifically recognize nonreducing structures of heparan sulfates. Beyond the pathology of Alzheimer’s disease, the members of the amyloid precursor protein (APP) family are essential for neuronal development and cell homeostasis in mammals. APP and its paralogues APP-like protein 1 (APLP1) and APP-like protein 2 (APLP2) contain the highly conserved heparan sulfate (HS) binding domain E2, which effects various (patho)physiological functions. Here, two crystal structures of the E2 domain of APLP1 are presented in the apo form and in complex with a heparin dodecasaccharide at 2.5 Å resolution. The apo structure of APLP1 E2 revealed an unfolded and hence flexible N-terminal helix αA. The (APLP1 E2){sub 2}–(heparin){sub 2} complex structure revealed two distinct binding modes, with APLP1 E2 explicitly recognizing the heparin terminus but also interacting with a continuous heparin chain. The latter only requires a certain register of the sugar moieties that fits to a positively charged surface patch and contributes to the general heparin-binding capability of APP-family proteins. Terminal binding of APLP1 E2 to heparin specifically involves a structure of the nonreducing end that is very similar to heparanase-processed HS chains. These data reveal a conserved mechanism for the binding of APP-family proteins to HS and imply a specific regulatory role of HS modifications in the biology of APP and APP-like proteins.

  1. A smart flow measurement system for flow evaluation with multiple signals in different operation modes

    NASA Astrophysics Data System (ADS)

    Kaltsas, G.; Katsikogiannis, P.; Asimakopoulos, P.; Nassiopoulou, A. G.

    2007-11-01

    This paper presents the development and evaluation of a smart flow measurement system based on an integrated thermal flow sensor that implements a heater and two pairs of thermopiles, symmetrically situated on both sides of the heater. A specially designed interface circuit monitors and controls sensor operation, allowing three different operational modes: constant voltage (CV), constant power (CP) and constant temperature (CT). It also simultaneously monitors the heater resistance and the thermopile signal. Communication with a PC is implemented through a USB connection, and a developed Java program controls the system and data representation and storage. Transfer rates in the order of 20 000 sps are achieved, which allow detailed flow monitoring. For system evaluation, flow measurements were performed in both the calorimetric and hot-wire principles with the three different modes of operation and the corresponding results are presented comparatively. Flow velocity was determined by different sensor signals (heater resistance and power, thermopile signal) and the related sensitivities were extracted. Furthermore, it was verified that the system could detect the flow direction as well as the transition point from laminar to turbulent region.

  2. Strategies to reduce the configuration time for a powered knee and ankle prosthesis across multiple ambulation modes.

    PubMed

    Simon, Ann M; Fey, Nicholas P; Finucane, Suzanne B; Lipschutz, Robert D; Hargrove, Levi J

    2013-06-01

    Recently developed powered lower limb prostheses allow users to more closely mimic the kinematics and kinetics of non-amputee gait. However, configuring such a device, in particular a combined powered knee and ankle, for individuals with a transfemoral amputation is challenging. Previous attempts have relied on empirical tuning of all control parameters. This paper describes modified stance phase control strategies - which mimic the behavior of biological joints or depend on the instantaneous loads within the prosthesis - developed to reduce the number of control parameters that require individual tuning. Three individuals with unilateral transfemoral amputations walked with a powered knee and ankle prosthesis across five ambulation modes (level ground walking, ramp ascent/descent, and stair ascent/descent). Starting with a nominal set of impedance parameters, the modified control strategies were applied and the devices were individually tuned such that all subjects achieved comfortable and safe ambulation. The control strategies drastically reduced the number of independent parameters that needed to be tuned for each subject (i.e., to 21 parameters instead of a possible 140 or approximately 4 parameters per mode) while relative amplitudes and timing of kinematic and kinetic data remained similar to those previously reported and to those of non-amputee subjects. Reducing the time necessary to configure a powered device across multiple ambulation modes may allow users to more quickly realize the benefits such powered devices can provide.

  3. A multiple gap plasma cathode electron gun and its electron beam analysis in self and trigger breakdown modes

    NASA Astrophysics Data System (ADS)

    Kumar, Niraj; Pal, Dharmendra Kumar; Jadon, Arvind Singh; Pal, Udit Narayan; Rahaman, Hasibur; Prakash, Ram

    2016-03-01

    In the present paper, a pseudospark discharge based multiple gap plasma cathode electron gun is reported which has been operated separately in self and trigger breakdown modes using two different gases, namely, argon and hydrogen. The beam current and beam energy have been analyzed using a concentric ring diagnostic arrangement. Two distinct electron beams are clearly seen with hollow cathode and conductive phases. The hollow cathode phase has been observed for ˜50 ns where the obtained electron beam is having low beam current density and high energy. While in conductive phase it is high current density and low energy electron beam. It is inferred that in the hollow cathode phase the beam energy is more for the self breakdown case whereas the current density is more for the trigger breakdown case. The tailor made operation of the hollow cathode phase electron beam can play an important role in microwave generation. Up to 30% variation in the electron beam energy has been achieved keeping the same gas and by varying the breakdown mode operations. Also, up to 32% variation in the beam current density has been achieved for the trigger breakdown mode at optimized trigger position by varying the gas type.

  4. A multiple gap plasma cathode electron gun and its electron beam analysis in self and trigger breakdown modes.

    PubMed

    Kumar, Niraj; Pal, Dharmendra Kumar; Jadon, Arvind Singh; Pal, Udit Narayan; Rahaman, Hasibur; Prakash, Ram

    2016-03-01

    In the present paper, a pseudospark discharge based multiple gap plasma cathode electron gun is reported which has been operated separately in self and trigger breakdown modes using two different gases, namely, argon and hydrogen. The beam current and beam energy have been analyzed using a concentric ring diagnostic arrangement. Two distinct electron beams are clearly seen with hollow cathode and conductive phases. The hollow cathode phase has been observed for ∼50 ns where the obtained electron beam is having low beam current density and high energy. While in conductive phase it is high current density and low energy electron beam. It is inferred that in the hollow cathode phase the beam energy is more for the self breakdown case whereas the current density is more for the trigger breakdown case. The tailor made operation of the hollow cathode phase electron beam can play an important role in microwave generation. Up to 30% variation in the electron beam energy has been achieved keeping the same gas and by varying the breakdown mode operations. Also, up to 32% variation in the beam current density has been achieved for the trigger breakdown mode at optimized trigger position by varying the gas type.

  5. A real-time plane-wave decomposition algorithm for characterizing perforated liners damping at multiple mode frequencies.

    PubMed

    Zhao, Dan

    2011-03-01

    Perforated liners with a narrow frequency range are widely used as acoustic dampers to stabilize combustion systems. When the frequency of unstable modes present in the combustion system is within the effective frequency range, the liners can efficiently dissipate acoustic waves. The fraction of the incident waves being absorbed (known as power absorption coefficient) is generally used to characterize the liners damping. To estimate it, plane waves either side of the liners need to be decomposed and characterized. For this, a real-time algorithm is developed. Emphasis is being placed on its ability to online decompose plane waves at multiple mode frequencies. The performance of the algorithm is evaluated first in a numerical model with two unstable modes. It is then experimentally implemented in an acoustically driven pipe system with a lined section attached. The acoustic damping of perforated liners is continuously characterized in real-time. Comparison is then made between the results from the algorithm and those from the short-time fast Fourier transform (FFT)-based techniques, which are typically used in industry. It was found that the real-time algorithm allows faster tracking of the liners damping, even when the forcing frequency was suddenly changed.

  6. A Dual-Mode Bandpass Filter with Multiple Controllable Transmission-Zeros Using T-Shaped Stub-Loaded Resonators

    PubMed Central

    Yao, Zh.; Wang, C.; Kim, N. Y.

    2014-01-01

    A dual-mode broadband bandpass filter (BPF) with multiple controllable transmission-zeros using T-shaped stub-loaded resonators (TSSLRs) is presented. Due to the symmetrical plane, the odd-even-mode theory can be adopted to characterize the BPF. The proposed filter consists of a dual-mode TSSLR and two modified feed-lines, which introduce two capacitive and inductive source-load (S-L) couplings. Five controllable transmission zeros (TZs) can be achieved for the high selectivity and the wide stopband because of the tunable amount of coupling capacitance and inductance. The center frequency of the proposed BPF is 5.8 GHz, with a 3 dB fraction bandwidth of 8.9%. The measured insertion and return losses are 1.75 and 28.18 dB, respectively. A compact size and second harmonic frequency suppression can be obtained by the proposed BPF with S-L couplings. PMID:24688406

  7. Multiple modes of chromatin configuration at natural meiotic recombination hot spots in fission yeast.

    PubMed

    Hirota, Kouji; Steiner, Walter W; Shibata, Takehiko; Ohta, Kunihiro

    2007-11-01

    The ade6-M26 meiotic recombination hot spot of fission yeast is defined by a cyclic AMP-responsive element (CRE)-like heptanucleotide sequence, 5'-ATGACGT-3', which acts as a binding site for the Atf1/Pcr1 heterodimeric transcription factor required for hot spot activation. We previously demonstrated that the local chromatin around the M26 sequence motif alters to exhibit higher sensitivity to micrococcal nuclease before the initiation of meiotic recombination. In this study, we have examined whether or not such alterations in chromatin occur at natural meiotic DNA double-strand break (DSB) sites in Schizosaccharomyces pombe. At one of the most prominent DSB sites, mbs1 (meiotic break site 1), the chromatin structure has a constitutively accessible configuration at or near the DSB sites. The establishment of the open chromatin state and DSB formation are independent of the CRE-binding transcription factor, Atf1. Analysis of the chromatin configuration at CRE-dependent DSB sites revealed both differences from and similarities to mbs1. For example, the tdh1+ locus, which harbors a CRE consensus sequence near the DSB site, shows a meiotically induced open chromatin configuration, similar to ade6-M26. In contrast, the cds1+ locus is similar to mbs1 in that it exhibits a constitutive open configuration. Importantly, Atf1 is required for the open chromatin formation in both tdh1+ and cds1+. These results suggest that CRE-dependent meiotic chromatin changes are intrinsic processes related to DSB formation in fission yeast meiosis. In addition, the results suggest that the chromatin configuration in natural meiotic recombination hot spots can be classified into at least three distinct categories: (i) an Atf1-CRE-independent constitutively open chromatin configuration, (ii) an Atf1-CRE-dependent meiotically induced open chromatin configuration, and (iii) an Atf1-CRE-dependent constitutively open chromatin configuration.

  8. Organic Anion Transporter 1 Is Inhibited by Multiple Mechanisms and Shows a Transport Mode Independent of Exchange.

    PubMed

    Hotchkiss, Adam G; Gao, Tiandai; Khan, Usman; Berrigan, Liam; Li, Mansong; Ingraham, Leslie; Pelis, Ryan M

    2015-12-01

    The mechanism by which drugs inhibit organic anion transporter 1 (OAT1) was examined. OAT1 was stably expressed in Chinese hamster ovary (CHO) cells, and para-aminohippurate (PAH) and 6-carboxyfluorescein were the substrates. Most compounds (10 of 14) inhibited competitively, increasing the Michaelis constant (Km) without affecting the maximal transport rate (Jmax). Others were mixed-type (lowering Jmax and increasing Km) or noncompetitive (lowering Jmax only) inhibitors. The interaction of a noncompetitive inhibitor (telmisartan) with OAT1 was examined further. Binding of telmisartan to OAT1 was observed, but translocation was not. Telmisartan did not alter the plasma membrane expression of OAT1, indicating that it lowers Jmax by reducing the turnover number. PAH transport after telmisartan treatment and its washout recovered faster in the presence of 10% fetal bovine serum in the washout buffer, indicating that binding of telmisartan to OAT1 and its inhibitory effect are reversible. Together, these data suggest that telmisartan binds reversibly to a site distinct from substrate and stabilizes the transporter in a conformation unfavorable for translocation. In the absence of an exchangeable extracellular substrate, PAH efflux from CHO-OAT1 cells was relatively rapid. Telmisartan slowed PAH efflux, suggesting that some transporter-mediated efflux occurs independent of exchange. Although drug-drug interaction predictions at OAT1 assume competitive inhibition, these data show that OAT1 can be inhibited by other mechanisms, which could influence the accuracy of drug-drug interaction predictions at the transporter. Telmisartan was useful for examining how a noncompetitive inhibitor can alter OAT1 transport activity and for uncovering a transport mode independent of exchange.

  9. A diffusion model for drying of a heat sensitive solid under multiple heat input modes.

    PubMed

    Sun, Lan; Islam, Md Raisul; Ho, J C; Mujumdar, A S

    2005-09-01

    To obtain optimal drying kinetics as well as quality of the dried product in a batch dryer, the energy required may be supplied by combining different modes of heat transfer. In this work, using potato slice as a model heat sensitive drying object, experimental studies were conducted using a batch heat pump dryer designed to permit simultaneous application of conduction and radiation heat. Four heat input schemes were compared: pure convection, radiation-coupled convection, conduction-coupled convection and radiation-conduction-coupled convection. A two-dimensional drying model was developed assuming the drying rate to be controlled by liquid water diffusion. Both drying rates and temperatures within the slab during drying under all these four heat input schemes showed good accord with measurements. Radiation-coupled convection is the recommended heat transfer scheme from the viewpoint of high drying rate and low energy consumption.

  10. Computational modeling of the Fc αRI receptor binding in the Fc α domain of the human antibody IgA: Normal Modes Analysis (NMA) study

    NASA Astrophysics Data System (ADS)

    Jayasinghe, Manori; Posgai, Monica; Tonddast-Navaei, Sam; Ibrahim, George; Stan, George; Herr, Andrew; George Stan Group Collaboration; Herr's Group Team

    2014-03-01

    Fc αRI receptor binding in the Fc α domain of the antibody IgA triggers immune effector responses such as phagocytosis and antibody-dependent cell-mediated cytotoxicity in eukaryotic cells. Fc α is a dimer of heavy chains of the IgA antibody and each Fc α heavy chain which consisted of two immunoglobulin constant domains, CH2 and CH3, can bind one Fc αRI molecule at the CH2-CH3 interface forming a 2:1 stoichiometry. Experimental evidences confirmed that Fc αRI binding to the Fc α CH2-CH3 junction altered the kinetics of HAA lectin binding at the distant IgA1 hinge. Our focus in this research was to understand the conformational changes and the network of residues which co-ordinate the receptor binding dynamics of the Fc α dimer complex. Structure-based elastic network modeling was used to compute normal modes of distinct Fc α configurations. Asymmetric and un-liganded Fc α configurations were obtained from the high resolution crystal structure of Fc α-Fc αRI 2:1 symmetric complex of PDB ID 1OW0. Our findings confirmed that Fc αRI binding, either in asymmetric or symmetric complex with Fc α, propagated long-range conformational changes across the Fc domains, potentially also impacting the distant IgA1 hinge.

  11. Mode of encapsulation of linezolid by β-cyclodextrin and its role in bovine serum albumin binding.

    PubMed

    Natesan, Sudha; Sowrirajan, Chandrasekaran; Yousuf, Sameena; Enoch, Israel V M V

    2015-01-22

    We describe, in this article, the associative interaction between Linezolid and β-Cyclodextrin, and the influence of β-Cyclodextrin on Linezolid's binding to Bovine serum albumin. β-Cyclodextrin forms a 1:1 inclusion complex with Linezolid, with a binding constant value of 3.51×10(2)M(-1). The binding is studied using ultraviolet-visible absorption, fluorescence, nuclear magnetic resonance, and rotating-frame overhauser effect spectroscopic techniques. The amide substituent on the oxazolidinone ring of Linezolid is involved in its binding to β-Cyclodextrin. The binding of the Linezolid to bovine serum albumin, in the absence and the presence of β-Cyclodextrin, is studied by analyzing the fluorescence quenching and Förster resonance energy transfer. The Stern-Volmer quenching constant, the binding constant, and energy transfer occurring on the interaction of the Linezolid with BSA are found to be smaller in the presence of β-Cyclodextrin than in water.

  12. Effects of multiple resistive shells and transient electromagnetic torque on the dynamics of mode locking in reversed field pinch plasmas

    NASA Astrophysics Data System (ADS)

    Guo, S. C.; Chu, M. S.

    2002-11-01

    The effects of multiple resistive shells and transient electromagnetic torque on the dynamics of mode locking in the reversed field pinch (RFP) plasmas are studied. Most RFP machines are equipped with one or more metal shells outside of the vacuum vessel. These shells have finite resistivities. The eddy currents induced in each of the shells contribute to the braking electromagnetic (EM) torque which slows down the plasma rotation. In this work we study the electromagnetic torque acting on the plasma (tearing) modes produced by a system of resistive shells. These shells may consist of several nested thin shells or several thin shells enclosed within a thick shell. The dynamics of the plasma mode is investigated by balancing the EM torque from the resistive shells with the plasma viscous torque. Both the steady state theory and the time-dependent theory are developed. The steady state theory is shown to provide an accurate account of the resultant EM torque if (dω/dt)ω-2≪1 and the time scale of interest is much longer than the response (L/R) time of the shell. Otherwise, the transient theory should be adopted. As applications, the steady state theory is used to evaluate the changes of the EM torque response from the resistive shells in two variants of two RFP machines: (1) modification from Reversed Field Experiment (RFX) [Gnesotto et al., Fusion Eng. Des. 25, 335 (1995)] to the modified RFX: both of them are equipped with one thin shell plus one thick shell; (2) modification from Extrap T2 to Extrap T2R [Brunsell et al., Plasma Phys. Controlled Fusion 43, 1457 (2001)]: both of them are equipped with two thin shells. The transient theory has been applied numerically to study the time evolution of the EM torque during the unlocking of a locked tearing mode in the modified RFX.

  13. Can beating between different dynamo modes explain multiple magnetic cycles in solar - type stars

    NASA Astrophysics Data System (ADS)

    Simoniello, R.; Karoff, C.; Metcalfe, T. S.

    2015-09-01

    Stellar magnetic activity can be characterized by a chaotic, multiple or single cycle behavior. Sometimes cyclic activity can be interrupted by a flat behavior. The mechanism that produce such a diverse behavior in stellar atmosphere is a matter of debate. We decided to address this issue by investigating the properties of a sample of 40 stars with high quality cycles, selected from the original data provided by the Mount Wilson Observatory. This sample contains stars with single and secondary cycles, whose secondary periods are longer or shorter than the primary cycle.

  14. The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding

    PubMed Central

    Keller, Heidi; Kiosze, Kristin; Sachsenweger, Juliane; Haumann, Sebastian; Ohlenschläger, Oliver; Nuutinen, Tarmo; Syväoja, Juhani E.; Görlach, Matthias; Grosse, Frank; Pospiech, Helmut

    2014-01-01

    Human RecQL4 belongs to the ubiquitous RecQ helicase family. Its N-terminal region represents the only homologue of the essential DNA replication initiation factor Sld2 of Saccharomyces cerevisiae, and also participates in the vertebrate initiation of DNA replication. Here, we utilized a random screen to identify N-terminal fragments of human RecQL4 that could be stably expressed in and purified from Escherichia coli. Biophysical characterization of these fragments revealed that the Sld2 homologous RecQL4 N-terminal domain carries large intrinsically disordered regions. The N-terminal fragments were sufficient for the strong annealing activity of RecQL4. Moreover, this activity appeared to be the basis for an ATP-independent strand exchange activity. Both activities relied on multiple DNA-binding sites with affinities to single-stranded, double-stranded and Y-structured DNA. Finally, we found a remarkable affinity of the N-terminus for guanine quadruplex (G4) DNA, exceeding the affinities for other DNA structures by at least 60-fold. Together, these findings suggest that the DNA interactions mediated by the N-terminal region of human RecQL4 represent a central function at the replication fork. The presented data may also provide a mechanistic explanation for the role of elements with a G4-forming propensity identified in the vicinity of vertebrate origins of DNA replication. PMID:25336622

  15. Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus

    PubMed Central

    Lu, Shih-Jen; Chong, Fok-Ching

    2012-01-01

    Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular dynamics simulations combined with the solvated interaction energies technique was applied to predict the docking models of the inhibitors in the binding pocket of the H1N1 influenza neuraminidase. In the simulations, the correlation of the predicted and experimental binding free energies of all 20 flavonoid derivatives inhibitors is satisfactory, as indicated by R2 = 0.75. PMID:22605992

  16. Synthesis of analogues of a flexible thiopyrylium photosensitizer for purging blood-borne pathogens and binding mode and affinity studies of their complexes with DNA.

    PubMed

    McKnight, Ruel E; Ye, Mao; Ohulchanskyy, Tymish Y; Sahabi, Sadia; Wetzel, Bryan R; Wagner, Stephen J; Skripchenko, Andrey; Detty, Michael R

    2007-07-01

    A series of thio- and selenopyrylium analogues of 2,4-di(4-dimethylaminophen-yl)-6-methylthiopyrylium iodide were prepared in five steps from 4-dimethylaminophenyl-propargyl aldehyde and the corresponding lithium acetylide. When bound to DNA, all of the dyes absorb at wavelengths >600nm, which avoids the hemoglobin band I maximum at 575nm. The binding of the series of dyes to double-stranded DNA was examined spectrophotometrically and by isothermal titration calorimetry to determine binding constants, by a topoisomerase I DNA unwinding assay, by competition dialysis with [poly(dGdC)](2) and [poly(dAdT)](2), and by ethidium bromide displacement studies to examine propensities for intercalation, and by circular dichroism studies. The dyes were found to show mixed binding modes.

  17. Structure optimization of 2-benzamidobenzoic acids as PqsD inhibitors for Pseudomonas aeruginosa infections and elucidation of binding mode by SPR, STD NMR, and molecular docking.

    PubMed

    Weidel, Elisabeth; de Jong, Johannes C; Brengel, Christian; Storz, Michael P; Braunshausen, Andrea; Negri, Matthias; Plaza, Alberto; Steinbach, Anke; Müller, Rolf; Hartmann, Rolf W

    2013-08-08

    Pseudomonas aeruginosa employs a characteristic pqs quorum sensing (QS) system that functions via the signal molecules PQS and its precursor HHQ. They control the production of a number of virulence factors and biofilm formation. Recently, we have shown that sulfonamide substituted 2-benzamidobenzoic acids, which are known FabH inhibitors, are also able to inhibit PqsD, the enzyme catalyzing the last and key step in the biosynthesis of HHQ. Here, we describe the further optimization and characterization of this class of compounds as PqsD inhibitors. Structural modifications showed that both the carboxylic acid ortho to the amide and 3'-sulfonamide are essential for binding. Introduction of substituents in the anthranilic part of the molecule resulted in compounds with IC50 values in the low micromolar range. Binding mode investigations by SPR with wild-type and mutated PqsD revealed that this compound class does not bind into the active center of PqsD but in the ACoA channel, preventing the substrate from accessing the active site. This binding mode was further confirmed by docking studies and STD NMR.

  18. Symmetric caging formation for convex polygonal object transportation by multiple mobile robots based on fuzzy sliding mode control.

    PubMed

    Dai, Yanyan; Kim, YoonGu; Wee, SungGil; Lee, DongHa; Lee, SukGyu

    2016-01-01

    In this paper, the problem of object caging and transporting is considered for multiple mobile robots. With the consideration of minimizing the number of robots and decreasing the rotation of the object, the proper points are calculated and assigned to the multiple mobile robots to allow them to form a symmetric caging formation. The caging formation guarantees that all of the Euclidean distances between any two adjacent robots are smaller than the minimal width of the polygonal object so that the object cannot escape. In order to avoid collision among robots, the parameter of the robots radius is utilized to design the caging formation, and the A⁎ algorithm is used so that mobile robots can move to the proper points. In order to avoid obstacles, the robots and the object are regarded as a rigid body to apply artificial potential field method. The fuzzy sliding mode control method is applied for tracking control of the nonholonomic mobile robots. Finally, the simulation and experimental results show that multiple mobile robots are able to cage and transport the polygonal object to the goal position, avoiding obstacles.

  19. Multiple player tracking in sports video: a dual-mode two-way bayesian inference approach with progressive observation modeling.

    PubMed

    Xing, Junliang; Ai, Haizhou; Liu, Liwei; Lao, Shihong

    2011-06-01

    Multiple object tracking (MOT) is a very challenging task yet of fundamental importance for many practical applications. In this paper, we focus on the problem of tracking multiple players in sports video which is even more difficult due to the abrupt movements of players and their complex interactions. To handle the difficulties in this problem, we present a new MOT algorithm which contributes both in the observation modeling level and in the tracking strategy level. For the observation modeling, we develop a progressive observation modeling process that is able to provide strong tracking observations and greatly facilitate the tracking task. For the tracking strategy, we propose a dual-mode two-way Bayesian inference approach which dynamically switches between an offline general model and an online dedicated model to deal with single isolated object tracking and multiple occluded object tracking integrally by forward filtering and backward smoothing. Extensive experiments on different kinds of sports videos, including football, basketball, as well as hockey, demonstrate the effectiveness and efficiency of the proposed method.

  20. Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites

    PubMed Central

    Jajamovich, Guido H.; Wang, Xiaodong; Arkin, Adam P.; Samoilov, Michael S.

    2011-01-01

    Finding conserved motifs in genomic sequences represents one of essential bioinformatic problems. However, achieving high discovery performance without imposing substantial auxiliary constraints on possible motif features remains a key algorithmic challenge. This work describes BAMBI—a sequential Monte Carlo motif-identification algorithm, which is based on a position weight matrix model that does not require additional constraints and is able to estimate such motif properties as length, logo, number of instances and their locations solely on the basis of primary nucleotide sequence data. Furthermore, should biologically meaningful information about motif attributes be available, BAMBI takes advantage of this knowledge to further refine the discovery results. In practical applications, we show that the proposed approach can be used to find sites of such diverse DNA-binding molecules as the cAMP receptor protein (CRP) and Din-family site-specific serine recombinases. Results obtained by BAMBI in these and other settings demonstrate better statistical performance than any of the four widely-used profile-based motif discovery methods: MEME, BioProspector with BioOptimizer, SeSiMCMC and Motif Sampler as measured by the nucleotide-level correlation coefficient. Additionally, in the case of Din-family recombinase target site discovery, the BAMBI-inferred motif is found to be the only one functionally accurate from the underlying biochemical mechanism standpoint. C++ and Matlab code is available at http://www.ee.columbia.edu/~guido/BAMBI or http://genomics.lbl.gov/BAMBI/. PMID:21948794

  1. Coexistence of multiple minor states of fatty acid binding protein and their functional relevance

    PubMed Central

    Yu, Binhan; Yang, Daiwen

    2016-01-01

    Proteins are dynamic over a wide range of timescales, but determining the number of distinct dynamic processes and identifying functionally relevant dynamics are still challenging. Here we present the study on human intestinal fatty acid binding protein (hIFABP) using a novel analysis of 15N relaxation dispersion (RD) and chemical shift saturation transfer (CEST) experiments. Through combined analysis of the two types of experiments, we found that hIFABP exists in a four-state equilibrium in which three minor states interconvert directly with the major state. According to conversion rates from the major “closed” state to minor states, these minor states are irrelevant to the function of fatty acid transport. Based on chemical shifts of the minor states which could not be determined from RD data alone but were extracted from a combined analysis of RD and CEST data, we found that all the minor states are native-like. This conclusion is further supported by hydrogen-deuterium exchange experiments. Direct conversions between the native state and native-like intermediate states may suggest parallel multitrack unfolding/folding pathways of hIFABP. Moreover, hydrogen-deuterium exchange data indicate the existence of another locally unfolded minor state that is relevant to the fatty acid entry process. PMID:27677899

  2. Multiple nucleic acid cleavage modes in divergent type III CRISPR systems

    PubMed Central

    Zhang, Jing; Graham, Shirley; Tello, Agnes; Liu, Huanting; White, Malcolm F.

    2016-01-01

    CRISPR-Cas is an RNA-guided adaptive immune system that protects bacteria and archaea from invading nucleic acids. Type III systems (Cmr, Csm) have been shown to cleave RNA targets in vitro and some are capable of transcription-dependent DNA targeting. The crenarchaeon Sulfolobus solfataricus has two divergent subtypes of the type III system (Sso-IIID and a Cmr7-containing variant of Sso-IIIB). Here, we report that both the Sso-IIID and Sso-IIIB complexes cleave cognate RNA targets with a ruler mechanism and 6 or 12 nt spacing that relates to the organization of the Cas7 backbone. This backbone-mediated cleavage activity thus appears universal for the type III systems. The Sso-IIIB complex is also known to possess a distinct ‘UA’ cleavage mode. The predominant activity observed in vitro depends on the relative molar concentration of protein and target RNA. The Sso-IIID complex can cleave plasmid DNA targets in vitro, generating linear DNA products with an activity that is dependent on both the cyclase and HD nuclease domains of the Cas10 subunit, suggesting a role for both nuclease active sites in the degradation of double-stranded DNA targets. PMID:26801642

  3. Multiple-Component Crystal Fabric Measurements from Acoustically-Generated Normal Modes in Borehole

    NASA Astrophysics Data System (ADS)

    Kluskiewicz, D. J.; Waddington, E. D.; McCarthy, M.; Anandakrishnan, S.; Voigt, D.; Matsuoka, K.

    2014-12-01

    Sound wave velocities in ice are a proxy of crystal orientation fabric. Because p- and s-waves respectively travel faster and slower in the direction of an ice crystal c-axis, the velocities of these waves in a fabric are related to the clustering of ice crystal c-axes in the direction of wave propagation. Previous sonic logs at Dome C, NGRIP, WAIS, and NEEM have inferred a single component fabric description from the velocities of vertically-propagating p-waves around each ice core borehole. These records supplement thin-section measurements of crystal fabric by sampling larger numbers of crystals in a depth-continuous log. Observations of azimuthally anisotropic vertical-girdle fabrics at ice-core sites such as WAIS, NGRIP, and EDML underly a benefit for logging methods that are sensitive to such fabrics. We present a theoretical framework for using borehole flexural modes to measure azimuthal crystal-fabric anisotropy, and describe ongoing efforts to develop a sonic logging tool for this purpose. We also present data from p-wave logs and thin section measurements at the WAIS Divide, and describe how a flexural wave log could supplement the existing measurements.

  4. Wavelength-selective emitters with pyramid nanogratings enhanced by multiple resonance modes

    NASA Astrophysics Data System (ADS)

    Nguyen-Huu, Nghia; Pištora, Jaromír; Cada, Michael

    2016-04-01

    Binary gratings with high or low metal filling ratios in a grating region have been demonstrated as successful candidates in enhancing the emittance of emitters for thermophotovoltaics since they could support surface plasmons (SPs), the Rayleigh-Wood anomaly (RWA), or cavity resonance (CR) within their geometries. This work shows that combining a tungsten binary grating with a low and high filling ratio to form a pyramid grating can significantly increase the emittance, which is nearly perfect in the wavelength region from 0.6 to 1.72 μm, while being 0.1 at wavelengths longer than 2.5 μm. Moreover, the emittance spectrum of the hybrid tungsten grating is insensitive to the angle of incidence. The enhancement demonstrated by magnetic field and Poynting vector patterns is due to the interplay between SPs and RWA modes at short wavelengths, and CR at long wavelengths. Furthermore, a combined grating made of nickel is also proposed providing enhanced emittance in a wide angle of incidence.

  5. Wavelength-selective emitters with pyramid nanogratings enhanced by multiple resonance modes.

    PubMed

    Nguyen-Huu, Nghia; Pištora, Jaromír; Cada, Michael

    2016-04-15

    Binary gratings with high or low metal filling ratios in a grating region have been demonstrated as successful candidates in enhancing the emittance of emitters for thermophotovoltaics since they could support surface plasmons (SPs), the Rayleigh-Wood anomaly (RWA), or cavity resonance (CR) within their geometries. This work shows that combining a tungsten binary grating with a low and high filling ratio to form a pyramid grating can significantly increase the emittance, which is nearly perfect in the wavelength region from 0.6 to 1.72 μm, while being 0.1 at wavelengths longer than 2.5 μm. Moreover, the emittance spectrum of the hybrid tungsten grating is insensitive to the angle of incidence. The enhancement demonstrated by magnetic field and Poynting vector patterns is due to the interplay between SPs and RWA modes at short wavelengths, and CR at long wavelengths. Furthermore, a combined grating made of nickel is also proposed providing enhanced emittance in a wide angle of incidence.

  6. Optical anisotropy of cubic photonic crystals under conditions of multiple-mode light propagation

    NASA Astrophysics Data System (ADS)

    Ukleev, T. A.; Yurasova, D. I.; Shevchenko, N. N.; Sel'kin, A. V.

    2016-11-01

    Bragg reflection spectra of light are studied for opal-like photonic crystals made of polystyrene spheres. A resonant enhancement of reflectivity is observed in cross-polarization configuration of the analyzer and polarizer when varying the azimuthal orientation of a sample in respect to the incidence plane. The cross-polarization effect takes place at oblique incidence of light on the lateral (111) crystal plane with the plane of incidence being non-perpendicular to the inclined (11-1) crystal plane. The effect is shown to be due to the multiple Bragg diffraction of light when the resonant Bragg conditions are fulfilled at a certain angle of incidence and azimuth for the lateral and inclined crystal planes simultaneously.

  7. Structural insight into mode of binding of Meropenem to CTX-M-15 type β-lactamase.

    PubMed

    Maryam, Lubna; Khan, Asad U

    2017-03-01

    Among Enterobacteriaceae, CTX-M type extended spectrum beta lactamase confers potent hydrolytic activity against cephalosporin group of antibiotics. Strains producing CTX-M type beta lactamase enzymes, show high level of resistance against cefotaxime. Therefore carbapenem antibiotics are used against beta lactamase producing strains. Hence, this study was designed to understand an insight of molecular basis of CTX-M-15 interaction with meropenem, and its effect on CTX-M-15 efficiency. Clinical strain of Enterobacter cloacae (EC-15) was used to clone blaCTX-M-15 gene in E.coli BL21cells. The protein was then expressed and purified. Results showed that CTX-M-15 producing strains are susceptible to meropenem. It quenches the fluorescence of CTX-M-15 spontaneously with binding constant of the order of 10(3)M(-1). Meropenem binds on the active site of CTX-M-15, hydrogen bonded with four common amino acid residues of cefotaxime binding site, as revealed by molecular docking studies. Conformational change in the structure of CTX-M-15 was observed upon meropenem binding by CD spectroscopy. The catalytic efficiency of CTX-M-15 was decreased up to 4 times upon meropenem binding. Docking study shows that few amino acids of active site of enzyme are also involved in meropenem binding, hence substrate is difficult to bind on active site properly and does not get hydrolysed. Moreover, meropenem binding induces structural changes in CTX-M-15, making the enzyme less efficient.

  8. Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

    PubMed Central

    Lee, Bum-Kyu; Battenhouse, Anna; Louzada, Sandra; Yang, Fengtang; Dunham, Ian; Crawford, Gregory E.; Lieb, Jason D.; Durbin, Richard; Iyer, Vishwanath R.; Birney, Ewan

    2014-01-01

    Associating genetic variation with quantitative measures of gene regulation offers a way to bridge the gap between genotype and complex phenotypes. In order to identify quantitative trait loci (QTLs) that influence the binding of a transcription factor in humans, we measured binding of the multifunctional transcription and chromatin factor CTCF in 51 HapMap cell lines. We identified thousands of QTLs in which genotype differences were associated with differences in CTCF binding strength, hundreds of them confirmed by directly observable allele-specific binding bias. The majority of QTLs were either within 1 kb of the CTCF binding motif, or in linkage disequilibrium with a variant within 1 kb of the motif. On the X chromosome we observed three classes of binding sites: a minority class bound only to the active copy of the X chromosome, the majority class bound to both the active and inactive X, and a small set of female-specific CTCF sites associated with two non-coding RNA genes. In sum, our data reveal extensive genetic effects on CTCF binding, both direct and indirect, and identify a diversity of patterns of CTCF binding on the X chromosome. PMID:25411781

  9. Munc13-Like skMLCK Variants Cannot Mimic the Unique Calmodulin Binding Mode of Munc13 as Evidenced by Chemical Cross-Linking and Mass Spectrometry

    PubMed Central

    Herbst, Sabine; Maucher, Daniel; Schneider, Marian; Ihling, Christian H.; Jahn, Olaf; Sinz, Andrea

    2013-01-01

    Among the neuronal binding partners of calmodulin (CaM) are Munc13 proteins as essential presynaptic regulators that play a key role in synaptic vesicle priming and are crucial for presynaptic short-term plasticity. Recent NMR structural investigations of a CaM/Munc13-1 peptide complex have revealed an extended structure, which contrasts the compact structures of most classical CaM/target complexes. This unusual binding mode is thought to be related to the presence of an additional hydrophobic anchor residue at position 26 of the CaM binding motif of Munc13-1, resulting in a novel 1-5-8-26 motif. Here, we addressed the question whether the 1-5-8-26 CaM binding motif is a Munc13-related feature or whether it can be induced in other CaM targets by altering the motif's core residues. For this purpose, we chose skeletal muscle myosin light chain kinase (skMLCK) with a classical 1-5-8-14 CaM binding motif and constructed three skMLCK peptide variants mimicking Munc13-1, in which the hydrophobic anchor amino acid at position 14 was moved to position 26. Chemical cross-linking between CaM and skMLCK peptide variants combined with high-resolution mass spectrometry yielded insights into the peptides' binding modes. This structural comparison together with complementary binding data from surface plasmon resonance experiments revealed that skMLCK variants with an artificial 1-5-8-26 motif cannot mimic CaM binding of Munc13-1. Apparently, additional features apart from the spacing of the hydrophobic anchor residues are required to define the functional 1-5-8-26 motif of Munc13-1. We conclude that Munc13 proteins display a unique CaM binding behavior to fulfill their role as efficient presynaptic calcium sensors over broad range of Ca2+ concentrations. PMID:24130683

  10. Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+.

    PubMed

    Yang, Changwon; Jang, Soonmin; Pak, Youngshang

    2011-12-14

    Using all-atom molecular dynamics simulation in conjunction with umbrella sampling, we obtained the unfolding free energy and the force extension profiles of the thrombin binding DNA aptamer (15-TBA) in complex with Sr(2+) (Protein Data Bank code: 1RDE). The resulting potential of mean force (PMF) displays a multiple stepwise pattern with distinct plateau regions. The detailed analysis of the simulation result indicated that each plateau was created by the interplay of the metal ion interacting with self-arranging guanine bases and the successive uptakes of water molecules. The current PMF simulation provides a quantitative description of the unfolding process of 15-TBA DNA driven by stretching and gives molecular insight on its detailed changes of base pair interactions in the presence of the metal cation.

  11. An analysis of the binding of repressor protein ModE to modABCD (molybdate transport) operator/promoter DNA of Escherichia coli.

    PubMed

    Grunden, A M; Self, W T; Villain, M; Blalock, J E; Shanmugam, K T

    1999-08-20

    Expression of the modABCD operon in Escherichia coli, which codes for a molybdate-specific transporter, is repressed by ModE in vivo in a molybdate-dependent fashion. In vitro DNase I-footprinting experiments identified three distinct regions of protection by ModE-molybdate on the modA operator/promoter DNA, GTTATATT (-15 to -8; region 1), GCCTACAT (-4 to +4; region 2), and GTTACAT (+8 to +14; region 3). Within the three regions of the protected DNA, a pentamer sequence, TAYAT (Y = C or T), can be identified. DNA-electrophoretic mobility experiments showed that the protected regions 1 and 2 are essential for binding of ModE-molybdate to DNA, whereas the protected region 3 increases the affinity of the DNA to the repressor. The stoichiometry of this interaction was found to be two ModE-molybdate per modA operator DNA. ModE-molybdate at 5 nM completely protected the modABCD operator/promoter DNA from DNase I-catalyzed hydrolysis, whereas ModE alone failed to protect the DNA even at 100 nM. The apparent K(d) for the interaction between the modA operator DNA and ModE-molybdate was 0.3 nM, and the K(d) increased to 8 nM in the absence of molybdate. Among the various oxyanions tested, only tungstate replaced molybdate in the repression of modA by ModE, but the affinity of ModE-tungstate for modABCD operator DNA was 6 times lower than with ModE-molybdate. A mutant ModE(T125I) protein, which repressed modA-lac even in the absence of molybdate, protected the same region of modA operator DNA in the absence of molybdate. The apparent K(d) for the interaction between modA operator DNA and ModE(T125I) was 3 nM in the presence of molybdate and 4 nM without molybdate. The binding of molybdate to ModE resulted in a decrease in fluorescence emission, indicating a conformational change of the protein upon molybdate binding. The fluorescence emission spectra of mutant ModE proteins, ModE(T125I) and ModE(Q216*), were unaffected by molybdate. The molybdate-independent mutant ModE

  12. The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development

    PubMed Central

    Alvarez, John D.; Yasui, Dag H.; Niida, Hiroyuki; Joh, Tadashi; Loh, Dennis Y.; Kohwi-Shigematsu, Terumi

    2000-01-01

    SATB1 is expressed primarily in thymocytes and can act as a transcriptional repressor. SATB1 binds in vivo to the matrix attachment regions (MARs) of DNA, which are implicated in the loop domain organization of chromatin. The role of MAR-binding proteins in specific cell lineages is unknown. We generated SATB1-null mice to determine how SATB1 functions in the T-cell lineage. SATB1-null mice are small in size, have disproportionately small thymi and spleens, and die at 3 weeks of age. At the cellular level, multiple defects in T-cell development were observed. Immature CD3−CD4−CD8− triple negative (TN) thymocytes were greatly reduced in number, and thymocyte development was blocked mainly at the DP stage. The few peripheral CD4+ single positive (SP) cells underwent apoptosis and failed to proliferate in response to activating stimuli. At the molecular level, among 589 genes examined, at least 2% of genes including a proto-oncogene, cytokine receptor genes, and apoptosis-related genes were derepressed at inappropriate stages of T-cell development in SATB1-null mice. For example, IL-2Rα and IL-7Rα genes were ectopically transcribed in CD4+CD8+ double positive (DP) thymocytes. SATB1 appears to orchestrate the temporal and spatial expression of genes during T-cell development, thereby ensuring the proper development of this lineage. Our data provide the first evidence that MAR-binding proteins can act as global regulators of cell function in specific cell lineages. PMID:10716941

  13. Detection and Tracking of Multiple Microbubbles in Ultrasound B-Mode Images.

    PubMed

    Ackermann, Dimitri; Schmitz, Georg

    2016-01-01

    The imaging of microvessels and the quantification of their blood flow is of particular interest in the characterization of tumor vasculature. The imaging resolution (50-200 μm) of high-frequency ultrasound (US) (20-50 MHz) is not sufficient to image microvessels (~10 μm) and Doppler sensitivity is not high enough to measure capillary blood flow (~1 mm/s). For imaging of blood flow in microvessels, our approach is to detect single microbubbles (MBs), track them over several frames, and to estimate their velocity. First, positions of MBs will be detected by separating B-mode frames in a moving foreground and a static background. For the crucial task of association of these positions to tracks, we implemented a modified Markov chain Monte Carlo data association (MCMCDA) algorithm, which can handle a high number of MBs. False alarms, the detection, initiation, and termination of MBs tracks are incorporated in the underlying model. To test the performance of algorithms, a US imaging simulation of a vessel tree with flowing MBs was set up (resolution 148 μm). The trajectories and flow velocity in the vessels with a lateral distance of 100 μm were reconstructed with super-resolution. In a phantom experiment, a suspension of MBs was pumped through a tube (diameter 0.4 mm) at speeds of 2.2, 4.2, 6.3, and 10.5 mm/s and was imaged with a Vevo2100 system (Visualsonics). Estimated mean speeds of the MBs were 2.1, 4.7, 7, and 10.5 mm/s. To demonstrate the applicability for in vivo measurements, a tumor xenograft-bearing mouse was imaged by this approach. The tumor vasculature was visualized with higher resolution than in a maximum intensity persistence image and the velocity values were in the expected range 0-1 mm/s.

  14. Unidirectional, dual-comb lasing under multiple pulse formation mechanisms in a passively mode-locked fiber ring laser.

    PubMed

    Liu, Ya; Zhao, Xin; Hu, Guoqing; Li, Cui; Zhao, Bofeng; Zheng, Zheng

    2016-09-19

    Dual-comb lasers simultaneously generating asynchronous ultrashort pulses could be an intriguing alternative to the current dual-laser comb source. When generated through a common light path, the low common-mode noises and good coherence between the pulse trains could be realized. Here we demonstrate the completely common-path, unidirectional dual-comb lasing using a carbon nanotube saturable absorber with additional pulse narrowing and broadening mechanisms. The interactions between multiple soliton formation mechanisms result in bifurcation into unusual two-pulse states with pulses of four-fold bandwidth difference and tens-of-Hz repetition rate difference. Coherence between the pulses is verified by the asynchronous cross-sampling and dual-comb spectroscopy measurements.

  15. Tempo and mode of the multiple origins of salinity tolerance in a water beetle lineage.

    PubMed

    Arribas, Paula; Andújar, Carmelo; Abellán, Pedro; Velasco, Josefa; Millán, Andrés; Ribera, Ignacio

    2014-02-01

    Salinity is one of the most important drivers of the distribution, abundance and diversity of organisms. Previous studies on the evolution of saline tolerance have been mainly centred on marine and terrestrial organisms, while lineages inhabiting inland waters remain largely unexplored. This is despite the fact that these systems include a much broader range of salinities, going from freshwater to more than six times the salinity of the sea (i.e. >200 g/L). Here, we study the pattern and timing of the evolution of the tolerance to salinity in an inland aquatic lineage of water beetles (Enochrus species of the subgenus Lumetus, family Hydrophilidae), with the general aim of understanding the mechanisms by which it was achieved. Using a time-calibrated phylogeny built from five mitochondrial and two nuclear genes and information about the salinity tolerance and geographical distribution of the species, we found that salinity tolerance appeared multiple times associated with periods of global aridification. We found evidence of some accelerated transitions from freshwater directly to high salinities, as reconstructed with extant lineages. This, together with the strong positive correlation found between salinity tolerance and aridity of the habitats in which species are found, suggests that tolerance to salinity may be based on a co-opted mechanism developed originally for drought resistance.

  16. The Vα14 invariant natural killer T cell TCR forces microbial glycolipids and CD1d into a conserved binding mode

    PubMed Central

    Li, Yali; Girardi, Enrico; Wang, Jing; Yu, Esther Dawen; Painter, Gavin F.; Kronenberg, Mitchell

    2010-01-01

    Invariant natural killer T cells (iNKT cells) rapidly produce effector cytokines. In this study, we report the first crystal structures of the iNKT cell T cell receptor (TCR) bound to two natural, microbial glycolipids presented by CD1d. Binding of the TCR induced CDR3-α–dependent structural changes in the F′ roof of CD1d; these changes resemble those occurring in the absence of TCR engagement when the highly potent synthetic antigen α-galactosylceramide (α-GalCer) binds CD1d. Furthermore, in the Borrelia burgdorferi α–galactosyl diacylglycerol–CD1d complex, TCR binding caused a marked repositioning of the galactose sugar into an orientation that closely resembles α-GalCer. The TCR-dependent reorientation of the sugar, together with the induced CD1d fit, may explain the weaker potency of the microbial antigens compared with α-GalCer. We propose that the TCR of iNKT cells binds with a conserved footprint onto CD1d, regardless of the bound glycolipid antigen, and that for microbial antigens this unique binding mode requires TCR-initiated conformational changes. PMID:20921281

  17. Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors

    PubMed Central

    Hsieh, Tung-Ju; Lin, Hsien-Ya; Tu, Zhijay; Lin, Ting-Chien; Wu, Shang-Chuen; Tseng, Yu-Yao; Liu, Fu-Tong; Hsu, Shang-Te Danny; Lin, Chun-Hung

    2016-01-01

    Human galectins are promising targets for cancer immunotherapeutic and fibrotic disease-related drugs. We report herein the binding interactions of three thio-digalactosides (TDGs) including TDG itself, TD139 (3,3’-deoxy-3,3’-bis-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside, recently approved for the treatment of idiopathic pulmonary fibrosis), and TAZTDG (3-deoxy-3-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside) with human galectins-1, -3 and -7 as assessed by X-ray crystallography, isothermal titration calorimetry and NMR spectroscopy. Five binding subsites (A–E) make up the carbohydrate-recognition domains of these galectins. We identified novel interactions between an arginine within subsite E of the galectins and an arene group in the ligands. In addition to the interactions contributed by the galactosyl sugar residues bound at subsites C and D, the fluorophenyl group of TAZTDG preferentially bound to subsite B in galectin-3, whereas the same group favored binding at subsite E in galectins-1 and -7. The characterised dual binding modes demonstrate how binding potency, reported as decreased Kd values of the TDG inhibitors from μM to nM, is improved and also offer insights to development of selective inhibitors for individual galectins. PMID:27416897

  18. Pharmacological properties and predicted binding mode of arylmethylene quinuclidine-like derivatives at the α3β4 nicotinic acetylcholine receptor (nAChR).

    PubMed

    Kombo, David C; Hauser, Terry A; Grinevich, Vladimir P; Melvin, Matthew S; Strachan, Jon-Paul; Sidach, Serguei S; Chewning, Joseph; Fedorov, Nikolai; Tallapragada, Kartik; Breining, Scott R; Miller, Craig H

    2013-03-01

    We have carried out a pharmacological evaluation of arylmethylene quinuclidine derivatives interactions with human α3β4 nAChRs subtype, using cell-based receptor binding, calcium-influx, electrophysiological patch-clamp assays and molecular modeling techniques. We have found that the compounds bind competitively to the α3β4 receptor with micromolar affinities and some of the compounds behave as non-competitive antagonists (compounds 1, 2 and 3), displaying submicromolar IC(50) values. These evidences suggest a mixed mode of action for these compounds, having interactions at the orthosteric site and more pronounced interactions at an allosteric site to block agonist effects. One of the compounds, 1-benzyl-3-(diphenylmethylene)-1-azoniabicyclo[2.2.2]octane chloride (compound 3), exhibited poorly reversible use-dependent block of α3β4 channels. We also found that removal of a phenyl group from compound 1 confers a partial agonism to the derived analog (compound 6). Introducing a hydrogen-bond acceptor into the 3-benzylidene quinuclidine derivative (compound 7) increases agonism potency at the α3β4 receptor subtype. Docking into the orthosteric binding site of a α3β4 protein structure derived by comparative modeling accurately predicted the experimentally-observed trend in binding affinity. Results supported the notion that binding requires a hydrogen bond formation between the ligand basic nitrogen and the backbone carbonyl oxygen atom of the conserved Trp-149.

  19. Silica uptake by Spartina-evidence of multiple modes of accumulation from salt marshes around the world.

    PubMed

    Carey, Joanna C; Fulweiler, Robinson W

    2014-01-01

    Silicon (Si) plays a critical role in plant functional ecology, protecting plants from multiple environmental stressors. While all terrestrial plants contain some Si, wetland grasses are frequently found to have the highest concentrations, although the mechanisms driving Si accumulation in wetland grasses remain in large part uncertain. For example, active Si accumulation is often assumed to be responsible for elevated Si concentrations found in wetland grasses. However, life stage and differences in Si availability in the surrounding environment also appear to be important variables controlling the Si concentrations of wetland grasses. Here we used original data from five North American salt marshes, as well as all known published literature values, to examine the primary drivers of Si accumulation in Spartina, a genus of prolific salt marsh grasses found worldwide. We found evidence of multiple modes of Si accumulation in Spartina, with passive accumulation observed in non-degraded marshes where Spartina was native, while rejective accumulation was found in regions where Spartina was invasive. Evidence of active accumulation was found in only one marsh where Spartina was native, but was also subjected to nutrient over-enrichment. We developed a conceptual model which hypothesizes that the mode of Si uptake by Spartina is dependent on local environmental factors and genetic origin, supporting the idea that plant species should be placed along a spectrum of Si accumulation. We hypothesize that Spartina exhibits previously unrecognized phenotypic plasticity with regard to Si accumulation, allowing these plants to respond to changes in marsh condition. These results provide new insight regarding how salt marsh ecosystems regulate Si exchange at the land-sea interface.

  20. Silica uptake by Spartina—evidence of multiple modes of accumulation from salt marshes around the world

    PubMed Central

    Carey, Joanna C.; Fulweiler, Robinson W.

    2014-01-01

    Silicon (Si) plays a critical role in plant functional ecology, protecting plants from multiple environmental stressors. While all terrestrial plants contain some Si, wetland grasses are frequently found to have the highest concentrations, although the mechanisms driving Si accumulation in wetland grasses remain in large part uncertain. For example, active Si accumulation is often assumed to be responsible for elevated Si concentrations found in wetland grasses. However, life stage and differences in Si availability in the surrounding environment also appear to be important variables controlling the Si concentrations of wetland grasses. Here we used original data from five North American salt marshes, as well as all known published literature values, to examine the primary drivers of Si accumulation in Spartina, a genus of prolific salt marsh grasses found worldwide. We found evidence of multiple modes of Si accumulation in Spartina, with passive accumulation observed in non-degraded marshes where Spartina was native, while rejective accumulation was found in regions where Spartina was invasive. Evidence of active accumulation was found in only one marsh where Spartina was native, but was also subjected to nutrient over-enrichment. We developed a conceptual model which hypothesizes that the mode of Si uptake by Spartina is dependent on local environmental factors and genetic origin, supporting the idea that plant species should be placed along a spectrum of Si accumulation. We hypothesize that Spartina exhibits previously unrecognized phenotypic plasticity with regard to Si accumulation, allowing these plants to respond to changes in marsh condition. These results provide new insight regarding how salt marsh ecosystems regulate Si exchange at the land-sea interface. PMID:24904599

  1. Search for supersolidity in solid 4He using multiple-mode torsional oscillators

    NASA Astrophysics Data System (ADS)

    Eyal, Anna; Mi, Xiao; Talanov, Artem V.; Reppy, John D.

    2016-06-01

    In 2004, Kim and Chan (KC) reported a decrease in the period of torsional oscillators (TO) containing samples of solid 4He, as the temperature was lowered below 0.2 K [Kim E, Chan MHW (2004) Science 305(5692):1941-1944]. These unexpected results constituted the first experimental evidence that the long-predicted supersolid state of solid 4He may exist in nature. The KC results were quickly confirmed in a number of other laboratories and created great excitement in the low-temperature condensed-matter community. Since that time, however, it has become clear that the period shifts seen in the early experiments can in large part be explained by an increase in the shear modulus of the 4He solid identified by Day and Beamish [Day J, Beamish J (2007) Nature 450(7171):853-856]. Using multiple-frequency torsional oscillators, we can separate frequency-dependent period shifts arising from changes in the elastic properties of the solid 4He from possible supersolid signals, which are expected to be independent of frequency. We find in our measurements that as the temperature is lowered below 0.2 K, a clear frequency-dependent contribution to the period shift arising from changes in the 4He elastic properties is always present. For all of the cells reported in this paper, however, there is always an additional small frequency-independent contribution to the total period shift, such as would be expected in the case of a transition to a supersolid state.

  2. Search for supersolidity in solid 4He using multiple-mode torsional oscillators

    PubMed Central

    Eyal, Anna; Mi, Xiao; Talanov, Artem V.; Reppy, John D.

    2016-01-01

    In 2004, Kim and Chan (KC) reported a decrease in the period of torsional oscillators (TO) containing samples of solid 4He, as the temperature was lowered below 0.2 K [Kim E, Chan MHW (2004) Science 305(5692):1941–1944]. These unexpected results constituted the first experimental evidence that the long-predicted supersolid state of solid 4He may exist in nature. The KC results were quickly confirmed in a number of other laboratories and created great excitement in the low-temperature condensed-matter community. Since that time, however, it has become clear that the period shifts seen in the early experiments can in large part be explained by an increase in the shear modulus of the 4He solid identified by Day and Beamish [Day J, Beamish J (2007) Nature 450(7171):853–856]. Using multiple-frequency torsional oscillators, we can separate frequency-dependent period shifts arising from changes in the elastic properties of the solid 4He from possible supersolid signals, which are expected to be independent of frequency. We find in our measurements that as the temperature is lowered below 0.2 K, a clear frequency-dependent contribution to the period shift arising from changes in the 4He elastic properties is always present. For all of the cells reported in this paper, however, there is always an additional small frequency-independent contribution to the total period shift, such as would be expected in the case of a transition to a supersolid state. PMID:27222579

  3. Unbound position II in MXCXXC metallochaperone model peptides impacts metal binding mode and reactivity: Distinct similarities to whole proteins.

    PubMed

    Shoshan, Michal S; Dekel, Noa; Goch, Wojciech; Shalev, Deborah E; Danieli, Tsafi; Lebendiker, Mario; Bal, Wojciech; Tshuva, Edit Y

    2016-06-01

    The effect of position II in the binding sequence of copper metallochaperones, which varies between Thr and His, was investigated through structural analysis and affinity and oxidation kinetic studies of model peptides. A first Cys-Cu(I)-Cys model obtained for the His peptide at acidic and neutral pH, correlated with higher affinity and more rapid oxidation of its complex; in contrast, the Thr peptide with the Cys-Cu(I)-Met coordination under neutral conditions demonstrated weaker and pH dependent binding. Studies with human antioxidant protein 1 (Atox1) and three of its mutants where S residues were replaced with Ala suggested that (a) the binding affinity is influenced more by the binding sequence than by the protein fold (b) pH may play a role in binding reactivity, and (c) mutating the Met impacted the affinity and oxidation rate more drastically than did mutating one of the Cys, supporting its important role in protein function. Position II thus plays a dominant role in metal binding and transport.

  4. Binding mode and thermodynamic studies on the interaction of the anticancer drug dacarbazine and dacarbazine-Cu(II) complex with single and double stranded DNA.

    PubMed

    Temerk, Yassien; Ibrahim, Hossieny

    2014-07-01

    The binding mode and thermodynamic characteristics of the anticancer drug dacarbazine (Dac) with double and single stranded DNA were investigated in the absence and presence of Cu(II) using cyclic voltammetry, square wave voltammetry and fluorescence spectroscopy. The interaction of Dac and Dac-Cu(II) complex with dsDNA indicated their intercalation into the base stacking domain of dsDNA double helix and the strength of interaction is independent on the ionic strength. The interaction of Dac with dsDNA in the presence of Cu(II) leads to a much stronger intercalation. The interaction mode of Dac molecules with ssDNA is electrostatic attraction via negative phosphate on the exterior of the ssDNA with Dac. The binding constants, stoichiometric coefficients and thermodynamic parameters of Dac and Dac-Cu(II) complex with dsDNA and ssDNA were evaluated. Comparison of the mode interaction of Dac with dsDNA and ssDNA was discussed. The decrease of peak current of Dac was proportional to DNA concentration, which was applied for determination of dsDNA and ssDNA concentration.

  5. A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of DNA G-Quadruplex Binding Mode

    PubMed Central

    Zhou, Yi-Wei; Wang, Hanqiang; Cao, Qian; Shen, Yong; Ji, Liang-Nian; Mao, Zong-Wan; Qin, Peter Z.

    2016-01-01

    We reported a novel strategy for investigating small molecule binding to G-quadruplexes (GQs). A newly synthesized dinuclear platinum(II) complex (Pt2L) containing a nitroxide radical was shown to selectively bind a GQ-forming sequence derived from human telomere (hTel). Using the nitroxide moiety as a spin label, electron paramagnetic resonance (EPR) spectroscopy was carried out to investigate binding between Pt2L and hTel GQ. Measurements indicated that two molecules of Pt2L bind with one molecule of hTel GQ. The inter-spin distance measured between the two bound Pt2L, together with molecular docking analyses, revealed that Pt2L predominately binds to the neighboring narrow and wide grooves of the G-tetrads as hTel adopts the antiparallel conformation. The design and synthesis of nitroxide tagged GQ binders, and the use of spin-labeling/EPR to investigate their interactions with GQs, will aid the development of small molecules for manipulating GQs involved in crucial biological processes. PMID:26845489

  6. Structure of Calmodulin Bound to a Calcineurin Peptide: A New Way of Making an Old Binding Mode

    SciTech Connect

    Ye,Q.; Li, X.; Wong, A.; Wei, Q.; Jia, Z.

    2006-01-01

    Calcineurin is a calmodulin-binding protein in brain and the only serine/threonine protein phosphatase under the control of Ca{sup 2+}/calmodulin (CaM), which plays a critical role in coupling Ca{sup 2+} signals to cellular responses. CaM up-regulates the phosphatase activity of calcineurin by binding to the CaM-binding domain (CBD) of calcineurin subunit A. Here, we report crystal structural studies of CaM bound to a CBD peptide. The chimeric protein containing CaM and the CBD peptide forms an intimate homodimer, in which CaM displays a native-like extended conformation and the CBD peptide shows -helical structure. Unexpectedly, the N-terminal lobe from one CaM and the C-terminal lobe from the second molecule form a combined binding site to trap the peptide. Thus, the dimer provides two binding sites, each of which is reminiscent of the fully collapsed conformation of CaM commonly observed in complex with, for example, the myosin light chain kinase (MLCK) peptide. The interaction between the peptide and CaM is highly specific and similar to MLCK.

  7. Mode of interaction of TRIP13 AAA-ATPase with the Mad2-binding protein p31comet and with mitotic checkpoint complexes

    PubMed Central

    Miniowitz-Shemtov, Shirly; Kaisari, Sharon; Sitry-Shevah, Danielle; Hershko, Avram

    2015-01-01

    The AAA-ATPase thyroid hormone receptor interacting protein 13 (TRIP13), jointly with the Mad2-binding protein p31comet, promotes the inactivation of the mitotic (spindle assembly) checkpoint by disassembling the mitotic checkpoint complex (MCC). This checkpoint system ensures the accuracy of chromosome segregation by delaying anaphase until correct bipolar attachment of chromatids to the mitotic spindle is achieved. MCC inhibits the anaphase-promoting complex/cyclosome (APC/C), a ubiquitin ligase that targets for degradation securin, an inhibitor of anaphase initiation. MCC is composed of the checkpoint proteins Mad2, BubR1, and Bub3, in association with the APC/C activator Cdc20. The assembly of MCC in active checkpoint is initiated by the conversion of Mad2 from an open (O-Mad2) to a closed (C-Mad2) conformation, which then binds tightly to Cdc20. Conversely, the disassembly of MCC that takes place when the checkpoint is turned off involves the conversion of C-Mad2 back to O-Mad2. Previously, we found that the latter process is mediated by TRIP13 together with p31comet, but the mode of their interaction remained unknown. Here, we report that the oligomeric form of TRIP13 binds both p31comet and MCC. Furthermore, p31comet and checkpoint complexes mutually promote the binding of each other to oligomeric TRIP13. We propose that p31comet bound to C-Mad2–containing checkpoint complex is the substrate for the ATPase and that the substrate-binding site of TRIP13 is composed of subsites specific for p31comet and C-Mad2–containing complex. The simultaneous occupancy of both subsites is required for high-affinity binding to TRIP13. PMID:26324890

  8. Multiple length peptide-pheromone variants produced by Streptococcus pyogenes directly bind Rgg proteins to confer transcriptional regulation.

    PubMed

    Aggarwal, Chaitanya; Jimenez, Juan Cristobal; Nanavati, Dhaval; Federle, Michael J

    2014-08-08

    Streptococcus pyogenes, a human-restricted pathogen, accounts for substantial mortality related to infections worldwide. Recent studies indicate that streptococci produce and respond to several secreted peptide signaling molecules (pheromones), including those known as short hydrophobic peptides (SHPs), to regulate gene expression by a quorum-sensing mechanism. Upon transport into the bacterial cell, pheromones bind to and modulate activity of receptor proteins belonging to the Rgg family of transcription factors. Previously, we reported biofilm regulation by the Rgg2/3 quorum-sensing circuit in S. pyogenes. The aim of this study was to identify the composition of mature pheromones from cell-free culture supernatants that facilitate biofilm formation. Bioluminescent reporters were employed to detect active pheromones in culture supernatants fractionated by reverse-phase chromatography, and mass spectrometry was used to characterize their properties. Surprisingly, multiple SHPs that varied by length were detected. Synthetic peptides of each variant were tested individually using bioluminescence reporters and biofilm growth assays, and although activities differed widely among the group, peptides comprising the C-terminal eight amino acids of the full-length native peptide were most active. Direct Rgg/SHP interactions were determined using a fluorescence polarization assay that utilized FITC-labeled peptide ligands. Peptide receptor affinities were seen to be as low as 500 nm and their binding affinities directly correlated with observed bioactivity. Revelation of naturally produced pheromones along with determination of their affinity for cognate receptors are important steps forward in designing compounds whose purpose is positioned for future therapeutics aimed at treating infections through the interference of bacterial communication.

  9. Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

    PubMed Central

    Palermo, Giulia; Bauer, Inga; Campomanes, Pablo; Cavalli, Andrea; Armirotti, Andrea; Girotto, Stefania; Rothlisberger, Ursula; De Vivo, Marco

    2015-01-01

    The fatty acid amide hydrolase (FAAH) regulates the endocannabinoid system cleaving primarily the lipid messenger anandamide. FAAH has been well characterized over the years and, importantly, it represents a promising drug target to treat several diseases, including inflammatory-related diseases and cancer. But its enzymatic mechanism for lipid selection to specifically hydrolyze anandamide, rather than similar bioactive lipids, remains elusive. Here, we clarify this mechanism in FAAH, examining the role of the dynamic paddle, which is formed by the gating residues Phe432 and Trp531 at the boundary between two cavities that form the FAAH catalytic site (the “membrane-access” and the “acyl chain-binding” pockets). We integrate microsecond-long MD simulations of wild type and double mutant model systems (Phe432Ala and Trp531Ala) of FAAH, embedded in a realistic membrane/water environment, with mutagenesis and kinetic experiments. We comparatively analyze three fatty acid substrates with different hydrolysis rates (anandamide > oleamide > palmitoylethanolamide). Our findings identify FAAH’s mechanism to selectively accommodate anandamide into a multi-pocket binding site, and to properly orient the substrate in pre-reactive conformations for efficient hydrolysis that is interceded by the dynamic paddle. Our findings therefore endorse a structural framework for a lipid selection mechanism mediated by structural flexibility and gating residues between multiple binding cavities, as found in FAAH. Based on the available structural data, this exquisite catalytic strategy for substrate specificity seems to be shared by other lipid-degrading enzymes with similar enzymatic architecture. The mechanistic insights for lipid selection might assist de-novo enzyme design or drug discovery efforts. PMID:26111155

  10. Targeting glutamine metabolism in multiple myeloma enhances BIM binding to BCL-2 eliciting synthetic lethality to venetoclax.

    PubMed

    Bajpai, R; Matulis, S M; Wei, C; Nooka, A K; Von Hollen, H E; Lonial, S; Boise, L H; Shanmugam, M

    2016-07-28

    Multiple myeloma (MM) is a plasma cell malignancy that is largely incurable due to development of resistance to therapy-elicited cell death. Nutrients are intricately connected to maintenance of cellular viability in part by inhibition of apoptosis. We were interested to determine if examination of metabolic regulation of BCL-2 proteins may provide insight on alternative routes to engage apoptosis. MM cells are reliant on glucose and glutamine and withdrawal of either nutrient is associated with varying levels of apoptosis. We and others have demonstrated that glucose maintains levels of key resistance-promoting BCL-2 family member, myeloid cell leukemic factor 1 (MCL-1). Cells continuing to survive in the absence of glucose or glutamine were found to maintain expression of MCL-1 but importantly induce pro-apoptotic BIM expression. One potential mechanism for continued survival despite induction of BIM could be due to binding and sequestration of BIM to alternate pro-survival BCL-2 members. Our investigation revealed that cells surviving glutamine withdrawal in particular, enhance expression and binding of BIM to BCL-2, consequently sensitizing these cells to the BH3 mimetic venetoclax. Glutamine deprivation-driven sensitization to venetoclax can be reversed by metabolic supplementation with TCA cycle intermediate α-ketoglutarate. Inhibition of glucose metabolism with the GLUT4 inhibitor ritonavir elicits variable cytotoxicity in MM that is marginally enhanced with venetoclax treatment, however, targeting glutamine metabolism with 6-diazo-5-oxo-l-norleucine uniformly sensitized MM cell lines and relapse/refractory patient samples to venetoclax. Our studies reveal a potent therapeutic strategy of metabolically driven synthetic lethality involving targeting glutamine metabolism for sensitization to venetoclax in MM.

  11. Multiple Length Peptide-Pheromone Variants Produced by Streptococcus pyogenes Directly Bind Rgg Proteins to Confer Transcriptional Regulation*

    PubMed Central

    Aggarwal, Chaitanya; Jimenez, Juan Cristobal; Nanavati, Dhaval; Federle, Michael J.

    2014-01-01

    Streptococcus pyogenes, a human-restricted pathogen, accounts for substantial mortality related to infections worldwide. Recent studies indicate that streptococci produce and respond to several secreted peptide signaling molecules (pheromones), including those known as short hydrophobic peptides (SHPs), to regulate gene expression by a quorum-sensing mechanism. Upon transport into the bacterial cell, pheromones bind to and modulate activity of receptor proteins belonging to the Rgg family of transcription factors. Previously, we reported biofilm regulation by the Rgg2/3 quorum-sensing circuit in S. pyogenes. The aim of this study was to identify the composition of mature pheromones from cell-free culture supernatants that facilitate biofilm formation. Bioluminescent reporters were employed to detect active pheromones in culture supernatants fractionated by reverse-phase chromatography, and mass spectrometry was used to characterize their properties. Surprisingly, multiple SHPs that varied by length were detected. Synthetic peptides of each variant were tested individually using bioluminescence reporters and biofilm growth assays, and although activities differed widely among the group, peptides comprising the C-terminal eight amino acids of the full-length native peptide were most active. Direct Rgg/SHP interactions were determined using a fluorescence polarization assay that utilized FITC-labeled peptide ligands. Peptide receptor affinities were seen to be as low as 500 nm and their binding affinities directly correlated with observed bioactivity. Revelation of naturally produced pheromones along with determination of their affinity for cognate receptors are important steps forward in designing compounds whose purpose is positioned for future therapeutics aimed at treating infections through the interference of bacterial communication. PMID:24958729

  12. Different modes of vancomycin and D-alanyl-D-alanine peptidase binding to cell wall peptide and a possible role for the vancomycin resistance protein.

    PubMed Central

    Knox, J R; Pratt, R F

    1990-01-01

    A comparison was made of the binding modes of the bacterial cell wall precursor L-lysyl-D-alanyl-D-alanine to the glycopeptide antibiotic vancomycin and to the D-alanyl-D-alanine-cleaving peptidase of Streptomyces sp. strain R61, a model for cell wall-synthesizing enzymes whose X-ray three-dimensional structure is established. In each of the two pairings (vancomycin with peptide and DD-peptidase with peptide), polypeptide backbones were antiparallel, and the antibiotic or enzyme enveloped the peptide substrate from opposite sides. Hydrogen-bonding groups on the substrate which are involved with the DD-peptidase were shown to be different from the ones reported from nuclear magnetic resonance studies to be involved with vancomycin. Because of steric hindrance, the binding of either molecule to the substrate prevents the binding of the other molecule. Binding to the substrate by a D-alanyl-D-alanine-recognizing protein in a manner similar to that used by the DD-peptidase could explain recent observations of vancomycin resistance, in which a new membrane-associated protein has been detected. PMID:2386365

  13. Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction*

    PubMed Central

    Sharadamma, Narayanaswamy; Harshavardhana, Yadumurthy; Ravishankar, Apoorva; Anand, Praveen; Chandra, Nagasuma; Muniyappa, K.

    2014-01-01

    The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ΔihfA and ΔihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHFαβ. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins. PMID:25324543

  14. Stimulus-response bindings code both abstract and specific representations of stimuli: evidence from a classification priming design that reverses multiple levels of response representation.

    PubMed

    Horner, A J; Henson, R N

    2011-11-01

    Repetition priming can be caused by the rapid retrieval of previously encoded stimulus-response (S-R) bindings. S-R bindings have recently been shown to simultaneously code multiple levels of response representation, from specific Motor-actions to more abstract Decisions ("yes"/"no") and Classifications (e.g., "man-made"/"natural"). Using an experimental design that reverses responses at all of these levels, we assessed whether S-R bindings also code multiple levels of stimulus representation. Across two experiments, we found effects of response reversal on priming when switching between object pictures and object names, consistent with S-R bindings that code stimuli at an abstract level. Nonetheless, the size of this reversal effect was smaller for such across-format (e.g., word-picture) repetition than for within-format (e.g., picture-picture) repetition, suggesting additional coding of format-specific stimulus representations. We conclude that S-R bindings simultaneously represent both stimuli and responses at multiple levels of abstraction.

  15. Crystal structure of RseB and a model of its binding mode to RseA

    PubMed Central

    Kim, Dong Young; Jin, Kyeong Sik; Kwon, Eunju; Ree, Moonhor; Kim, Kyeong Kyu

    2007-01-01

    The bacterial envelope stress response senses stress signals in the extracytoplasmic compartment, and activates σE-dependent transcription by degrading its antisigma factor RseA. RseB, a binding partner of RseA, plays a pivotal role in regulating this response, but its molecular mechanism is not understood. We therefore determined the crystal structure of Escherichia coli RseB at a resolution of 2.4 Å. RseB is composed of two domains linked by a flexible linker and forms a loosely packed dimer with two grooves on each side. This structural feature is confirmed by small-angle scattering in solution. Analysis of the binding of various RseA mutants to RseB allowed us to identify the major RseB-binding motif in RseA. These data, coupled with analysis of small-angle scattering of the RseA/RseB complex in solution, leads us to propose that two RseAs bind to the grooves of the dimeric RseB by conserved residues. The implications for modulating proteolytic cleavage of RseA are discussed. PMID:17496148

  16. Exploration of DNA binding mode, chemical nuclease, cytotoxic and apoptotic potentials of diketone based oxovanadium(IV) complexes.

    PubMed

    Inamdar, Poonam Rajiv; Sheela, Angappan

    2015-05-01

    Two diketone based oxovanadium complexes, viz., bis(4,4,4-trifluoro-1-phenylbutane-1,3-dionato)oxovanadium(IV) (1) and bis(1,1,1-trifluoropentane-2,4-dionato)oxovanadium(IV) (2), have been synthesized and characterized by spectroscopic and analytical techniques. The DNA binding and the cleaving ability of the complexes is assessed by UV-vis spectroscopy, fluorescence spectroscopy, viscometry and gel electrophoretic studies. The DNA binding constant values (Kb) are found to be 1.95 ± 0.16 × 10(3)M(-1) for complex 1 and 1.064 ± 0.17 × 10(3)M(-1) for complex 2, respectively. Based on the results of the spectral and viscosity studies, it is observed that the complexes, interestingly, have preferred minor groove binding with DNA. Further, the concentration-dependent oxidative cleavage pattern of pBR322 in the presence of the activating reagent, hydrogen peroxide, has also been discussed. In addition, the complexes have shown moderate cytotoxic activity by inducing apoptosis against the cervical cancer cell line, HeLa. The results of in silico analysis and logP predictions are found to be in good agreement with the experimental observations. Thus, synthesized oxovanadium complexes have displayed promising DNA binding behavior and DNA cleavage activity with moderately cytotoxic nature.

  17. sNASP and ASF1A function through both competitive and compatible modes of histone binding

    PubMed Central

    Bowman, Andrew; Koide, Akiko; Goodman, Jay S.; Colling, Meaghan E.; Zinne, Daria; Koide, Shohei; Ladurner, Andreas G.

    2017-01-01

    Histone chaperones are proteins that interact with histones to regulate the thermodynamic process of nucleosome assembly. sNASP and ASF1 are conserved histone chaperones that interact with histones H3 and H4 and are found in a multi-chaperoning complex in vivo. Previously we identified a short peptide motif within H3 that binds to the TPR domain of sNASP with nanomolar affinity. Interestingly, this peptide motif is sequestered within the known ASF1–H3–H4 interface, raising the question of how these two proteins are found in complex together with histones when they share the same binding site. Here, we show that sNASP contains at least two additional histone interaction sites that, unlike the TPR–H3 peptide interaction, are compatible with ASF1A binding. These surfaces allow ASF1A to form a quaternary complex with both sNASP and H3–H4. Furthermore, we demonstrate that sNASP makes a specific complex with H3 on its own in vitro, but not with H4, suggesting that it could work upstream of ASF1A. Further, we show that sNASP and ASF1A are capable of folding an H3–H4 dimer in vitro under native conditions. These findings reveal a network of binding events that may promote the entry of histones H3 and H4 into the nucleosome assembly pathway. PMID:28123037

  18. Inhibition and Larvicidal Activity of Phenylpropanoids from Piper sarmentosum on Acetylcholinesterase against Mosquito Vectors and Their Binding Mode of Interaction

    PubMed Central

    Hematpoor, Arshia; Liew, Sook Yee; Chong, Wei Lim; Azirun, Mohd Sofian; Lee, Vannajan Sanghiran; Awang, Khalijah

    2016-01-01

    Aedes aegypti, Aedes albopictus and Culex quinquefasciatus are vectors of dengue fever and West Nile virus diseases. This study was conducted to determine the toxicity, mechanism of action and the binding interaction of three active phenylpropanoids from Piper sarmentosum (Piperaceae) toward late 3rd or early 4th larvae of above vectors. A bioassay guided-fractionation on the hexane extract from the roots of Piper sarmentosum led to the isolation and identification of three active phenylpropanoids; asaricin 1, isoasarone 2 and trans-asarone 3. The current study involved evaluation of the toxicity and acetylcholinesterase (AChE) inhibition of these compounds against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae. Asaricin 1 and isoasarone 2 were highly potent against Aedes aegypti, Aedes albopictus and Culex quinquefasciatus larvae causing up to 100% mortality at ≤ 15 μg/mL concentration. The ovicidal activity of asaricin 1, isoasarone 2 and trans-asarone 3 were evaluated through egg hatching. Asaricin 1 and isoasarone 2 showed potent ovicidal activity. Ovicidal activity for both compounds was up to 95% at 25μg/mL. Asaricin 1 and isoasarone 2 showed strong inhibition on acetylcholinesterase with relative IC50 values of 0.73 to 1.87 μg/mL respectively. These findings coupled with the high AChE inhibition may suggest that asaricin 1 and isoasarone 2 are neuron toxic compounds toward Aedes aegypti, Aedes albopictus and Culex quinquefasciatus. Further computational docking with Autodock Vina elaborates the possible interaction of asaricin 1 and isoasarone 2 with three possible binding sites of AChE which includes catalytic triads (CAS: S238, E367, H480), the peripheral sites (PAS: E72, W271) and anionic binding site (W83). The binding affinity of asaricin 1 and isoasarone 2 were relatively strong with asaricin 1 showed a higher binding affinity in the anionic pocket. PMID:27152416

  19. Synthesis, cytotoxic activities and proposed mode of binding of a series of bis([(9-oxo-9,10-dihydroacridine-4-carbonyl)amino]alkyl) alkylamines.

    PubMed

    Braña, Miguel F; Casarrubios, Luis; Domínguez, Gema; Fernández, Carlos; Pérez, José M; Quiroga, Adoración G; Navarro-Ranninger, Carmen; de Pascual-Teresa, Beatriz

    2002-04-01

    A series of bis([(9-oxo-9,10-dihydroacridine-4-carbonyl)amino]alkyl) alkylamines have been prepared and their antiproliferative properties have been tested against HT-29 cell lines. Compounds 6b and 6d showed an interesting cytotoxic profile and were subjected to further cytotoxic evaluation, DNA binding properties and molecular modelling studies. The evaluation of the cytotoxic activity of compounds 6b and 6d against pairs of cisplatin-sensitive and -resistant ovarian tumour cells shows that both compounds may be endowed with interesting antitumour properties because they are able to circumvent cisplatin resistance in A2780cisR, CH1cisR and Pam 212-ras tumour cells. On the other hand, DNA binding data indicate that compounds 6b and 6d are able to intercalate stronger than acridine within the double helix. Both compounds displace ethidium bromide with an efficiency ten times higher than acridine from several linear double-stranded DNAs and induce 43 degrees unwinding in supercoiled pBR322 DNA while acridine unwinds pBR322 DNA by only 24 degrees. Altogether these data indicate that the significant conformational changes induced by compounds 6b and 6d in the double helix are due to a bis-intercalative DNA binding mode. We propose that binding to DNA through bisintercalation might be at least in part responsible for the remarkable cytotoxic properties of these acridine derivatives. The complex of 6b with d(GCGCGC)(2) in the four possible orientations that the ligand can adopt when binding to the DNA hexamer have been modelled and subjected to molecular dynamics simulations with the aim of evaluating the binding preferences of this bisintercalating agent into the DNA molecule. The predictions suggest that 6b binds to d(GCGCGC)(2) with a parallel orientation of the chromophores relative to each other and with a preference for binding through the minor groove of the hexamer. The possible relevance of these findings to the process of bisintercalation and the antitumour

  20. (S)-2-Amino-6-nitrohexanoic Acid Binds to Human Arginase I through Multiple Nitro−Metal Coordination Interactions in the Binuclear Manganese Cluster

    SciTech Connect

    Zakharian, T.; Di Costanzo, L; Christianson, D

    2008-01-01

    The binding affinity of (S)-2-amino-6-nitrohexanoic acid to human arginase I was studied using surface plasmon resonance (K{sub d} = 60 {mu}M), and the X-ray crystal structure of the enzyme-inhibitor complex was determined at 1.6 {angstrom} resolution to reveal multiple nitro-metal coordination interactions.

  1. Vitamin D Binding Protein Isoforms and Apolipoprotein E in Cerebrospinal Fluid as Prognostic Biomarkers of Multiple Sclerosis

    PubMed Central

    Lis, Katarzyna; Minari, Nicoletta; Falvo, Sara; Marnetto, Fabiana; Caldano, Marzia; Reviglione, Raffaella; Berchialla, Paola; Capobianco, Marco A.; Malentacchi, Maria; Corpillo, Davide; Bertolotto, Antonio

    2015-01-01

    Background Multiple sclerosis (MS) is a multifactorial autoimmune disease of the central nervous system with a heterogeneous and unpredictable course. To date there are no prognostic biomarkers even if they would be extremely useful for early patient intervention with personalized therapies. In this context, the analysis of inter-individual differences in cerebrospinal fluid (CSF) proteome may lead to the discovery of biological markers that are able to distinguish the various clinical forms at diagnosis. Methods To this aim, a two dimensional electrophoresis (2-DE) study was carried out on individual CSF samples from 24 untreated women who underwent lumbar puncture (LP) for suspected MS. The patients were clinically monitored for 5 years and then classified according to the degree of disease aggressiveness and the disease-modifying therapies prescribed during follow up. Results The hierarchical cluster analysis of 2-DE dataset revealed three protein spots which were identified by means of mass spectrometry as Apolipoprotein E (ApoE) and two isoforms of vitamin D binding protein (DBP). These three protein spots enabled us to subdivide the patients into subgroups correlated with clinical classification (MS aggressive forms identification: 80%). In particular, we observed an opposite trend of values for the two protein spots corresponding to different DBP isoforms suggesting a role of a post-translational modification rather than the total protein content in patient categorization. Conclusions These findings proved to be very interesting and innovative and may be developed as new candidate prognostic biomarkers of MS aggressiveness, if confirmed. PMID:26046356

  2. Multiple ATP-binding cassette transporters are involved in insecticide resistance in the small brown planthopper, Laodelphax striatellus.

    PubMed

    Sun, H; Pu, J; Chen, F; Wang, J; Han, Z

    2017-03-16

    ATP-binding cassette (ABC) transporters are membrane-bound proteins involved in the movement of various substrates, including drugs and insecticides, across the lipid membrane. Demonstration of the role of human ABC transporters in multidrug resistance has led to speculation that they might be an important mechanism controlling the fate of insecticides in insects. However, the role of ABC transporters in insects remains largely unknown. The small brown planthopper, Laodelphax striatellus Fallén, has developed resistance to most of the insecticides used for its control. Our goals were to identify the ABC transporters in La. striatellus and to examine their involvement in resistance mechanisms, using related strains resistant to chlorpyrifos, deltamethrin and imidacloprid, compared with the susceptible strain. Based on the transcriptome of La. striatellus, 40 full-length ABC transporters belonging to the ABCA-ABCH subfamilies were identified. Quantitative PCR revealed that over 20% of genes were significantly up-regulated in different resistant strains, and eight genes from the ABCB/C/D/G subfamilies were up-regulated in all three resistant strains, compared with the susceptible strain. Furthermore, synergism studies showed verapamil significantly enhanced insecticide toxicity in various resistant strains but not in the susceptible strain. These results suggest that ABC transporters might be involved in resistance to multiple insecticides in La. striatellus.

  3. Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps

    NASA Astrophysics Data System (ADS)

    Negri, Matthias; Recanatini, Maurizio; Hartmann, Rolf W.

    2011-09-01

    17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of estrogen-dependent diseases like breast cancer and endometriosis. 17β-HSD1 belongs to the bisubstrate enzymes and exists as an ensemble of conformations. These principally differ in the region of the βFαG'-loop, suggesting a prominent role in substrate and inhibitor binding. Although several classes of potent non-steroidal 17β-HSD1 inhibitors currently exist, their binding mode is still unclear. We aimed to elucidate the binding mode of bis(hydroxyphenyl)arenes, a highly potent class of 17β-HSD1 inhibitors, and to rank these compounds correctly with respect to their inhibitory potency, two essential aspects in drug design. Ensemble docking experiments resulted in a steroidal binding mode for the closed enzyme conformations and in an alternative mode for the opened and occluded conformers with the inhibitors placed below the NADPH interacting with it synergically via π-π stacking and H-bond formation. Both binding modes were investigated by MD simulations and MM-PBSA binding free energy estimations using as representative member for this class compound 1 (50 nM). Notably, only the alternative binding mode proved stable and was energetically more favorable, while when simulated in the steroidal binding mode compound 1 was displaced from the active site. In parallel, ab initio studies of small NADPH-inhibitor complexes were performed, which supported the importance of the synergistic interaction between inhibitors and cofactor.

  4. Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis.

    PubMed

    Dhakshnamoorthy, Balasundaresan; Mizuno, Hiroshi; Kumar, Penmetcha K R

    2013-09-01

    Anti-terminator proteins control gene expression by recognizing control signals within cognate transcripts and then preventing transcription termination. HutP is such a regulatory protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences in hut mRNAs. During the anti-termination process, l-histidine and a divalent ion are required for hutP to bind to the specific sequence within the hut mRNA. Our previous crystal structure of the HutP-l-histidine-Mg(2+)-RNA ternary complex demonstrated that the l-histidine ligand and Mg(2+) bind together such that the backbone nitrogen and carboxyl oxygen of l-histidine coordinate with Mg(2+). In addition to the Mg(2+), other divalent ions are also known to efficiently support the l-histidine-dependent anti-termination of the hut operon, and the best divalent ion is Zn(2+). In this study, we determined the crystal structure of the HutP-l-histidine-Zn(2+) complex and found that the orientation of l-histidine coordinated to Zn(2+) is reversed relative to that of l-histidine coordinated to Mg(2+), i.e., the imidazole side chain nitrogen of l-histidine coordinates to Zn(2+). This alternative binding mode of the l-histidine ligand to a divalent ion provides further insight into the mechanisms responsible for the activation of RNA binding during the hut anti-termination process.

  5. Graphene-Borate as an Efficient Fire Retardant for Cellulosic Materials with Multiple and Synergetic Modes of Action.

    PubMed

    Nine, Md J; Tran, Diana N H; Tung, Tran Thanh; Kabiri, Shervin; Losic, Dusan

    2017-03-10

    To address high fire risks of flamable cellulosic materials, that can trigger easy combustion, flame propagation, and release of toxic gases, we report a new fire-retardant approach using synergetic actions combining unique properties of reduced graphene oxide (rGO) and hydrated-sodium metaborates (SMB). The single-step treatment of cellulosic materials by a composite suspension of rGO/SMB was developed to create a barrier layer on sawdust surface providing highly effective fire retardant protection with multiple modes of action. These performances are designed considering synergy between properties of hydrated-SMB crystals working as chemical heat-sink to slow down the thermal degradation of the cellulosic particles and gas impermeable rGO layers that prevents access of oxygen and the release of toxic volatiles. The rGO outer layer also creates a thermal and physical barrier by donating carbon between the flame and unburnt wood particles. The fire-retardant performance of developed graphene-borate composite and mechanism of fire protection are demonstrated by testing of different forms of cellulosic materials such as pine sawdust, particle-board, and fiber-based structures. Results revealed their outstanding self-extinguishing behavior with significant resistance to release of toxic and flammable volatiles suggesting rGO/SMB to be suitable alternative to the conventional toxic halogenated flame-retardant materials.

  6. The Fort Collins Commuter Study: Impact of route type and transport mode on personal exposure to multiple air pollutants

    PubMed Central

    Good, Nicholas; Mölter, Anna; Ackerson, Charis; Bachand, Annette; Carpenter, Taylor; Clark, Maggie L; Fedak, Kristen M; Kayne, Ashleigh; Koehler, Kirsten; Moore, Brianna; L'Orange, Christian; Quinn, Casey; Ugave, Viney; Stuart, Amy L; Peel, Jennifer L; Volckens, John

    2016-01-01

    Traffic-related air pollution is associated with increased mortality and morbidity, yet few studies have examined strategies to reduce individual exposure while commuting. The present study aimed to quantify how choice of mode and route type affects personal exposure to air pollutants during commuting. We analyzed within-person difference in exposures to multiple air pollutants (black carbon (BC), carbon monoxide (CO), ultrafine particle number concentration (PNC), and fine particulate matter (PM2.5)) during commutes between the home and workplace for 45 participants. Participants completed 8 days of commuting by car and bicycle on direct and alternative (reduced traffic) routes. Mean within-person exposures to BC, PM2.5, and PNC were higher when commuting by cycling than when driving, but mean CO exposure was lower when cycling. Exposures to CO and BC were reduced when commuting along alternative routes. When cumulative exposure was considered, the benefits from cycling were attenuated, in the case of CO, or exacerbated, in the case of particulate exposures, owing to the increased duration of the commute. Although choice of route can reduce mean exposure, the effect of route length and duration often offsets these reductions when cumulative exposure is considered. Furthermore, increased ventilation rate when cycling may result in a more harmful dose than inhalation at a lower ventilation rate. PMID:26507004

  7. Parametric study of the damage ring pattern in fused silica induced by multiple longitudinal modes laser pulses

    SciTech Connect

    Chambonneau, M. Grua, P.; Rullier, J.-L.; Lamaignère, L.; Natoli, J.-Y.

    2015-03-14

    With the use of multiple longitudinal modes nanosecond laser pulses at 1064 nm, laser damage sites at the exit surface of fused silica clearly and systematically exhibit ring patterns. It has been shown in our previous works that the apparent chronology of rings was closely related to the temporal shape of the laser pulses. This particular correspondence had suggested an explanation of the ring morphology formation based on the displacement of an ionization front in the surrounding air. To provide a former basis for this hypothesis and deeper understanding of ring pattern formation, additional experiments have been performed. First, the impact of fluence has been investigated, revealing that a wide variety of damage sites are produced within a very narrow fluence range; this fact involves the chronology of appearance of a surface plasma during the laser pulse. The sizes of the damage sites are proportional to the fluence of their expansion occurring between the beginning of the plasma and the end of the laser pulse. Second, specific experiments have been carried out at different angles of incidence, resulting in egg-shaped patterns rather than circular ones. This behavior can be explained by our previous hypothesis of creation of a plasma in air, its expansion being tightly conditioned by the illumination angle. This series of experiments, in which the angle of incidence is varied up to 80°, permits us to link quantitatively the working hypothesis of ionization front propagation with theoretical hydrodynamics modeling.

  8. Parametric study of the damage ring pattern in fused silica induced by multiple longitudinal modes laser pulses

    NASA Astrophysics Data System (ADS)

    Chambonneau, M.; Grua, P.; Rullier, J.-L.; Natoli, J.-Y.; Lamaignère, L.

    2015-03-01

    With the use of multiple longitudinal modes nanosecond laser pulses at 1064 nm, laser damage sites at the exit surface of fused silica clearly and systematically exhibit ring patterns. It has been shown in our previous works that the apparent chronology of rings was closely related to the temporal shape of the laser pulses. This particular correspondence had suggested an explanation of the ring morphology formation based on the displacement of an ionization front in the surrounding air. To provide a former basis for this hypothesis and deeper understanding of ring pattern formation, additional experiments have been performed. First, the impact of fluence has been investigated, revealing that a wide variety of damage sites are produced within a very narrow fluence range; this fact involves the chronology of appearance of a surface plasma during the laser pulse. The sizes of the damage sites are proportional to the fluence of their expansion occurring between the beginning of the plasma and the end of the laser pulse. Second, specific experiments have been carried out at different angles of incidence, resulting in egg-shaped patterns rather than circular ones. This behavior can be explained by our previous hypothesis of creation of a plasma in air, its expansion being tightly conditioned by the illumination angle. This series of experiments, in which the angle of incidence is varied up to 80°, permits us to link quantitatively the working hypothesis of ionization front propagation with theoretical hydrodynamics modeling.

  9. Binding mode and potency of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors targeting Trypanosoma cruzi CYP51

    SciTech Connect

    Vieira, Debora F.; Choi, Jun Yong; Calvet, Claudia M.; Siqueira-Neto, Jair Lage; Johnston, Jonathan B.; Kellar, Danielle; Gut, Jiri; Cameron, Michael D.; McKerrow, James H.; Roush, William R.; Podust, Larissa M.

    2014-11-13

    Chagas disease is a chronic infection in humans caused by Trypanosoma cruzi and manifested in progressive cardiomyopathy and/or gastrointestinal dysfunction. Limited therapeutic options to prevent and treat Chagas disease put 8 million people infected with T. cruzi worldwide at risk. CYP51, involved in the biosynthesis of the membrane sterol component in eukaryotes, is a promising drug target in T. cruzi. We report the structure–activity relationships (SAR) of an N-arylpiperazine series of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors designed to probe the impact of substituents in the terminal N-phenyl ring on binding mode, selectivity and potency. Depending on the substituents at C-4, two distinct ring binding modes, buried and solvent-exposed, have been observed by X-ray structure analysis (resolution of 1.95–2.48 Å). Lastly, the 5-chloro-substituted analogs 9 and 10 with no substituent at C-4 demonstrated improved selectivity and potency, suppressing ≥99.8% parasitemia in mice when administered orally at 25 mg/kg, b.i.d., for 4 days.

  10. Binding of the auxiliary subunit TRIP8b to HCN channels shifts the mode of action of cAMP.

    PubMed

    Hu, Lei; Santoro, Bina; Saponaro, Andrea; Liu, Haiying; Moroni, Anna; Siegelbaum, Steven

    2013-12-01

    Hyperpolarization-activated cyclic nucleotide-regulated cation (HCN) channels generate the hyperpolarization-activated cation current Ih present in many neurons. These channels are directly regulated by the binding of cAMP, which both shifts the voltage dependence of HCN channel opening to more positive potentials and increases maximal Ih at extreme negative voltages where voltage gating is complete. Here we report that the HCN channel brain-specific auxiliary subunit TRIP8b produces opposing actions on these two effects of cAMP. In the first action, TRIP8b inhibits the effect of cAMP to shift voltage gating, decreasing both the sensitivity of the channel to cAMP (K1/2) and the efficacy of cAMP (maximal voltage shift); conversely, cAMP binding inhibits these actions of TRIP8b. These mutually antagonistic actions are well described by a cyclic allosteric mechanism in which TRIP8b binding reduces the affinity of the channel for cAMP, with the affinity of the open state for cAMP being reduced to a greater extent than the cAMP affinity of the closed state. In a second apparently independent action, TRIP8b enhances the action of cAMP to increase maximal Ih. This latter effect cannot be explained by the cyclic allosteric model but results from a previously uncharacterized action of TRIP8b to reduce maximal current through the channel in the absence of cAMP. Because the binding of cAMP also antagonizes this second effect of TRIP8b, application of cAMP produces a larger increase in maximal Ih in the presence of TRIP8b than in its absence. These findings may provide a mechanistic explanation for the wide variability in the effects of modulatory transmitters on the voltage gating and maximal amplitude of Ih reported for different neurons in the brain.

  11. Molecular dynamics simulation of tryptophan hydroxylase-1: binding modes and free energy analysis to phenylalanine derivative inhibitors.

    PubMed

    Zhong, Hao; Huang, Wei; He, Gu; Peng, Cheng; Wu, Fengbo; Ouyang, Liang

    2013-05-10

    Serotonin is a neurotransmitter that modulates many central and peripheral functions. Tryptophan hydroxylase-1 (TPH1) is a key enzyme of serotonin synthesis. In the current study, the interaction mechanism of phenylalanine derivative TPH1 inhibitors was investigated using molecular dynamics (MD) simulations, free energy calculations, free energy decomposition analysis and computational alanine scanning. The predicted binding free energies of these complexes are consistent with the experimental data. The analysis of the individual energy terms indicates that although the van der Waals and electrostatics interaction contributions are important in distinguishing the binding affinities of these inhibitors, the electrostatic contribution plays a more crucial role in that. Moreover, it is observed that different configurations of the naphthalene substituent could form different binding patterns with protein, yet lead to similar inhibitory potency. The combination of different molecular modeling techniques is an efficient way to interpret the interaction mechanism of inhibitors and our work could provide valuable information for the TPH1 inhibitor design in the future.

  12. The Structure of Sucrose Phosphate Synthase from Halothermothrix orenii Reveals Its Mechanism of Action and Binding Mode[W][OA

    PubMed Central

    Chua, Teck Khiang; Bujnicki, Janusz M.; Tan, Tien-Chye; Huynh, Frederick; Patel, Bharat K.; Sivaraman, J.

    2008-01-01

    Sucrose phosphate synthase (SPS) catalyzes the transfer of a glycosyl group from an activated donor sugar, such as uridine diphosphate glucose (UDP-Glc), to a saccharide acceptor d-fructose 6-phosphate (F6P), resulting in the formation of UDP and d-sucrose-6′-phosphate (S6P). This is a central regulatory process in the production of sucrose in plants, cyanobacteria, and proteobacteria. Here, we report the crystal structure of SPS from the nonphotosynthetic bacterium Halothermothrix orenii and its complexes with the substrate F6P and the product S6P. SPS has two distinct Rossmann-fold domains with a large substrate binding cleft at the interdomain interface. Structures of two complexes show that both the substrate F6P and the product S6P bind to the A-domain of SPS. Based on comparative analysis of the SPS structure with other related enzymes, the donor substrate, nucleotide diphosphate glucose, binds to the B-domain of SPS. Furthermore, we propose a mechanism of catalysis by H. orenii SPS. Our findings indicate that SPS from H. orenii may represent a valid model for the catalytic domain of plant SPSs and thus may provide useful insight into the reaction mechanism of the plant enzyme. PMID:18424616

  13. Interpretation of Ocular Melanin Drug Binding Assays. Alternatives to the Model of Multiple Classes of Independent Sites.

    PubMed

    Manzanares, José A; Rimpelä, Anna-Kaisa; Urtti, Arto

    2016-04-04

    Melanin has a high binding affinity for a wide range of drugs. The determination of the melanin binding capacity and its binding affinity are important, e.g., in the determination of the ocular drug distribution, the prediction of drug effects in the eye, and the trans-scleral drug delivery. The binding parameters estimated from a given data set vary significantly when using different isotherms or different nonlinear fitting methods. In this work, the commonly used bi-Langmuir isotherm, which assumes two classes of independent sites, is confronted with the Sips isotherm. Direct, log-log, and Scatchard plots are used, and the interpretation of the binding curves in the latter is critically analyzed. In addition to the goodness of fit, the emphasis is placed on the physical meaning of the binding parameters. The bi-Langmuir model imposes a bimodal distribution of binding energies for the sites on the melanin granules, but the actual distribution is most likely continuous and unimodal, as assumed by the Sips isotherm. Hence, the latter describes more accurately the distribution of binding energies and also the experimental results of melanin binding to drugs and metal ions. Simulations are used to show that the existence of two classes of sites cannot be confirmed on the sole basis of the shape of the binding curve in the Scatchard plot, and that serious doubts may appear on the meaning of the binding parameters of the bi-Langmuir model. Experimental results of melanin binding to chloroquine and metoprolol are used to illustrate the importance of the choice of the binding isotherm and of the method used to evaluate the binding parameters.

  14. Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.

    PubMed

    Lang, Julien; Vigouroux, Armelle; Planamente, Sara; El Sahili, Abbas; Blin, Pauline; Aumont-Nicaise, Magali; Dessaux, Yves; Moréra, Solange; Faure, Denis

    2014-10-01

    By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K(D) of 0.6 µM) greater than that for nopaline (KD of 3.7 µM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche

  15. Crystal structures of antibiotic-bound complexes of aminoglycoside 2''-phosphotransferase IVa highlight the diversity in substrate binding modes among aminoglycoside kinases.

    PubMed

    Shi, Kun; Houston, Douglas R; Berghuis, Albert M

    2011-07-19

    Aminoglycoside 2''-phosphotransferase IVa [APH(2'')-IVa] is a member of a family of bacterial enzymes responsible for medically relevant resistance to antibiotics. APH(2'')-IVa confers high-level resistance against several clinically used aminoglycoside antibiotics in various pathogenic Enterococcus species by phosphorylating the drug, thereby preventing it from binding to its ribosomal target and producing a bactericidal effect. We describe here three crystal structures of APH(2'')-IVa, one in its apo form and two in complex with a bound antibiotic, tobramycin and kanamycin A. The apo structure was refined to a resolution of 2.05 Å, and the APH(2'')-IVa structures with tobramycin and kanamycin A bound were refined to resolutions of 1.80 and 2.15 Å, respectively. Comparison among the structures provides insight concerning the substrate selectivity of this enzyme. In particular, conformational changes upon substrate binding, involving rotational shifts of two distinct segments of the enzyme, are observed. These substrate-induced shifts may also rationalize the altered substrate preference of APH(2'')-IVa in comparison to those of other members of the APH(2'') subfamily, which are structurally closely related. Finally, analysis of the interactions between the enzyme and aminoglycoside reveals a distinct binding mode as compared to the intended ribosomal target. The differences in the pattern of interactions can be utilized as a structural basis for the development of improved aminoglycosides that are not susceptible to these resistance factors.

  16. Molecular Docking and Binding Mode Analysis of Plant Alkaloids as in vitro and in silico Inhibitors of Trypanothione Reductase from Trypanosoma cruzi.

    PubMed

    Argüelles, Alonso J; Cordell, Geoffrey A; Maruenda, Helena

    2016-01-01

    Trypanothione reductase (TryR) is a key enzyme in the metabolism of Trypanosoma cruzi, the parasite responsible for Chagas disease. The available repertoire of TryR inhibitors relies heavily on synthetic substrates of limited structural diversity, and less on plant-derived natural products. In this study, a molecular docking procedure using a Lamarckian Genetic Algorithm was implemented to examine the protein-ligand binding interactions of strong in vitro inhibitors for which no X-ray data is available. In addition, a small, skeletally diverse, set of natural alkaloids was assessed computationally against T. cruzi TryR in search of new scaffolds for lead development. The preferential binding mode (low number of clusters, high cluster population), together with the deduced binding interactions were used to discriminate among the virtual inhibitors. This study confirms the prior in vitro data and proposes quebrachamine, cephalotaxine, cryptolepine, (22S,25S)-tomatidine, (22R,25S)-solanidine, and (22R,25R)-solasodine as new alkaloid scaffold leads in the search for more potent and selective TryR inhibitors.

  17. DNA interaction studies of a copper (II) complex containing an antiviral drug, valacyclovir: the effect of metal center on the mode of binding.

    PubMed

    Shahabadi, Nahid; Fatahi, Parvin

    2012-07-01

    The water-soluble complex, [Cu(Val)(2)(NO(3))(2)]; in which Val = valacyclovir, an antiviral drug, has been synthesized and characterized by elemental analysis, furier transfer-infrared, hydrogen nuclear magnetic resonance (H NMR), and UV-Vis techniques. The binding of this Cu (II) complex to calf thymus DNA was investigated using fluorimetry, spectrophotometry, circular dichroism, and viscosimetry. In fluorimetric studies, the enthalpy and entropy of the reaction between the complex and calf-thymus DNA (CT-DNA) showed that the reaction is endothermic (ΔH = 208.22 kJ mol(-1); ΔS = 851.35 J mol(-1)K(-1)). The complex showed the absorption hyperchromism in its ultra violet-visible (UV-Vis) spectrum with DNA. The calculated binding constant, K(b), obtained from UV-Vis absorption studies was 2 × 10(5) M(-1). Moreover, the complex induced detectable changes in the circular dichroism spectrum of CT-DNA, as well as changes in its viscosity. The results suggest that this copper (II) complex interacts with CT-DNA via a groove-binding mode.

  18. Multipose binding in molecular docking.

    PubMed

    Atkovska, Kalina; Samsonov, Sergey A; Paszkowski-Rogacz, Maciej; Pisabarro, M Teresa

    2014-02-14

    Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.

  19. Molecular interactions of DNA-topoisomerase I and II inhibitor with DNA and topoisomerases and in ternary complexes: binding modes and biological effects for intoplicine derivatives.

    PubMed

    Nabiev, I; Chourpa, I; Riou, J F; Nguyen, C H; Lavelle, F; Manfait, M

    1994-08-02

    Molecular interactions of intoplicine, dual DNA-topoisomerases (Topo) I and II inhibitor, with topoisomerases, plasmid DNA, in ternary cleavable complexes with enzymes and plasmid DNA, and in the reversed cleavable complexes were examined by means of surface-enhanced Raman scattering (SERS) and CD spectroscopy and by biochemical techniques. Detailed spectral analysis of intoplicine derivatives allowed us to assign SERS vibrational modes of chromophores and to propose the models for these complexes. Intoplicine was found to be able to interact specifically with the Topo II alone, but with Topo I only when in the presence of DNA. It shows at least two modes of binding to the DNA: the first was found to be dominant for its derivative 1c (most potent Topo I inhibitor), and the second was dominant for derivative 2a (most potent Topo II inhibitor). The possibility of forming these two types of complexes simultaneously is suggested to be one of the main factors enabling the drug to be a dual Topo I and Topo II inhibitor. The "deep intercalation mode" of the drug from the DNA minor groove with the long axis of the chromophore oriented roughly parallel to the dyad axis has been suggested to be responsible for induction of distortions of the DNA structure by the intercalating drug. Being involved in the formation of Topo I-mediated cleavable ternary complex, the molecules participating in the deep intercalation mode within the DNA do not change their molecular interactions as compared with their complex with the DNA alone. The stabilization of the Topo I-mediated cleavable complex was shown to be followed by the local denaturation of DNA in the AT-rich regions of the helix. When the ternary cleavable complex was reversed, the drug was shown to be in the complex with the plasmid. The "outside binding mode" from the DNA major groove via the hydroxyl group of the A-ring of the chromophore has been suggested to be responsible for Topo II inhibition. These molecules did not

  20. Structure of the Munc18c/Syntaxin4 N-peptide complex defines universal features of the N-peptide binding mode of Sec1/Munc18 proteins

    PubMed Central

    Hu, Shu-Hong; Latham, Catherine F.; Gee, Christine L.; James, David E.; Martin, Jennifer L.

    2007-01-01

    Sec1/Munc18 proteins (SM proteins) bind to soluble NSF attachment protein receptors (SNAREs) and play an essential role in membrane fusion. Divergent modes of regulation have been proposed for different SM proteins indicating that they can either promote or inhibit SNARE assembly. This is in part because of discrete modes of binding that have been described for various SM/SNARE complexes. One mode suggests that SM proteins bind only to Syntaxins (Stx) preventing SNARE assembly, whereas in another they facilitate SNARE assembly and bind to SNARE complexes. The mammalian cell surface SM protein Munc18c binds to an N-peptide in Stx4, and this is compatible with its interaction with SNARE complexes. Here we describe the crystal structure of Munc18c in complex with the Stx4 N-peptide. This structure shows remarkable similarity with a yeast complex indicating that the mode of binding, which can accommodate SNARE complexes, is highly conserved throughout evolution. Modeling reveals the presence of the N-peptide binding mode in most but not all yeast and mammalian SM/Stx pairs, suggesting that it has coevolved to fulfill a specific regulatory function. It is unlikely that the N-peptide interaction alone accounts for the specificity in SM/SNARE binding, implicating other contact surfaces in this function. Together with other data, our results support a sequential two-state model for SM/SNARE binding involving an initial interaction via the Stx N-peptide, which somehow facilitates a second, more comprehensive interaction comprising other contact surfaces in both proteins. PMID:17517664

  1. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode

    PubMed Central

    Qian, Tianle; Wo, Jing; Zhang, Yan; Song, Quanwei; Feng, Guoqiang; Luo, Ray; Lin, Shuangjin; Wu, Geng; Chen, Hai-Feng

    2017-01-01

    Streptonigrin methylesterase A (StnA) is one of the tailoring enzymes that modify the aminoquinone skeleton in the biosynthesis pathway of Streptomyces species. Although StnA has no significant sequence homology with the reported α/β-fold hydrolases, it shows typical hydrolytic activity in vivo and in vitro. In order to reveal its functional characteristics, the crystal structures of the selenomethionine substituted StnA (SeMet-StnA) and the complex (S185A mutant) with its substrate were resolved to the resolution of 2.71 Å and 2.90 Å, respectively. The overall structure of StnA can be described as an α-helix cap domain on top of a common α/β hydrolas